In [1]:
# Filepaths and Hard-coded Defaults

proj_root = "/users/kcochran/projects/procap_models/"
sequence_path = proj_root + "genomes/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
chrom_sizes = proj_root + "genomes/hg38.chrom.sizes.withrRNA"

in_window = 2114
out_window = 1000
In [2]:
# stuff to get from config file

with open("2022-07-05_09-52-52_run1_modisco_config.txt") as config_f:
    config_dict = {line.split()[0] : line.strip().split()[1] for line in config_f}

modisco_out_path = config_dict["modisco_out_path"]
scoring_type = config_dict["scoring_type"]
score_center_size = int(config_dict["score_center_size"])
profile_display_center_size = int(config_dict["profile_display_center_size"])

# digest what's in config file

assay_type, model_type, cell, accession, modisco_dir_base = modisco_out_path.split("/")[-5:]
ts_part1, ts_part2, run_str, _ = modisco_dir_base.split("_")
timestamp = ts_part1 + "_" + ts_part2
run = int(run_str.replace("run", ""))
In [3]:
print(modisco_out_path)
print("cell_type:", cell, accession)
print("timestamp:", timestamp)
print("run:", run)
print("scoring_type:", scoring_type)
print("score_center_size:", score_center_size)
print("profile_display_center_size:", profile_display_center_size)

/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco
cell_type: MCF10A ENCSR799DGV
timestamp: 2022-07-05_09-52-52
run: 1
scoring_type: counts
score_center_size: 1000
profile_display_center_size: 400
In [4]:
data_dir = proj_root + "/data/procap/processed/" + cell + "/" + accession + "/"
plus_bw_path = data_dir + "final.5prime.pos.bigWig"
minus_bw_path = data_dir + "final.5prime.neg.bigWig"
val_peak_path = data_dir + "peaks_uni_and_bi_train_and_val.bed.gz"

val_save_dir = proj_root + "model_out/" + assay_type + "/" + model_type + "/" + cell + "/" + accession + "/"
val_save_path = val_save_dir + timestamp + "_run" + str(run) + "_train_and_val"

attr_save_path = val_save_dir.replace("model_out", "deepshap_out") + timestamp + "_run" + str(run) + "_deepshap"

if not modisco_out_path.endswith("/"):
    modisco_out_path = modisco_out_path + "/"
In [5]:
# task-specific filepaths

import os

assert scoring_type in ["profile", "counts"], scoring_type

if scoring_type == "profile":
    scores_path = attr_save_path + "_prof.npy"
    onehot_scores_path = attr_save_path + "_prof_onehot.npy"
    modisco_obj_path = modisco_out_path + "results_allChroms_prof_slice500.hdf5"
    seqlet_path = modisco_out_path + "seqlets_prof.txt"
else:
    scores_path = attr_save_path + "_count.npy"
    onehot_scores_path = attr_save_path + "_count_onehot.npy"
    modisco_obj_path = modisco_out_path + "results_allChroms_count_slice500.hdf5"
    seqlet_path = modisco_out_path + "seqlets_count.txt"
    
assert(os.path.exists(scores_path)), scores_path
assert(os.path.exists(onehot_scores_path)), onehot_scores_path
In [6]:
# Imports, Plotting Defaults

import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager

plot_params = {
    "figure.titlesize": 22,
    "axes.titlesize": 22,
    "axes.labelsize": 20,
    "legend.fontsize": 18,
    "xtick.labelsize": 16,
    "ytick.labelsize": 16,
    "font.weight": "bold"
}
plt.rcParams.update(plot_params)

from IPython.display import display
import tqdm
tqdm.tqdm_notebook()

import numpy as np

from view_modisco_results_utils import *

/users/kcochran/miniconda3/envs/procap/lib/python3.7/site-packages/ipykernel_launcher.py:19: TqdmDeprecationWarning: This function will be removed in tqdm==5.0.0
Please use `tqdm.notebook.tqdm` instead of `tqdm.tqdm_notebook`
In [7]:
# Load in True Profiles and Sequences

import sys
sys.path.append('../1_train_models')

from data_loading import extract_peaks

one_hot_seqs, true_profs = extract_peaks(sequence_path, 
    plus_bw_path, minus_bw_path, val_peak_path, in_window, out_window,
    max_jitter=0, verbose=True)

one_hot_seqs = one_hot_seqs.swapaxes(1,2)
one_hot_seqs = one_hot_seqs[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]

Reading FASTA: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 24/24 [00:14<00:00,  1.63it/s]
Loading Peaks: 52007it [01:16, 680.14it/s]
In [8]:
# Load in Coordinates of Examples
    
coords = load_coords(val_peak_path, in_window)
In [9]:
# Import SHAP scores, predicted profiles

hyp_scores = np.load(scores_path).swapaxes(1,2)
hyp_scores = hyp_scores[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]
pred_profs = np.exp(np.load(val_save_path + ".profs.npy"))
In [10]:
# Load modisco results object
    
tfm_obj = import_tfmodisco_results(modisco_obj_path, hyp_scores, one_hot_seqs)
In [11]:
motif_pfms, motif_hcwms, motif_cwms, \
    motif_pfms_short, num_seqlets, \
    motif_seqlets, num_metaclusters = plot_all_metaclusters(tfm_obj, one_hot_seqs, hyp_scores,
                                                            true_profs, pred_profs, coords,
                                                            in_window, out_window,
                                                            score_center_size,
                                                            profile_display_center_size)

Metacluster 1/2

Pattern 1/34

14601 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 2/34

13270 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 3/34

12697 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 4/34

7051 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 5/34

5554 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 6/34

3986 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 7/34

2896 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 8/34

2753 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 9/34

2447 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 10/34

2250 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 11/34

1247 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 12/34

1103 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 13/34

1069 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 14/34

990 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 15/34

883 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 16/34

840 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 17/34

825 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 18/34

802 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 19/34

753 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 20/34

689 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 21/34

652 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 22/34

485 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 23/34

459 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 24/34

426 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 25/34

423 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 26/34

411 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 27/34

265 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 28/34

262 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 29/34

244 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 30/34

195 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 31/34

169 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 32/34

49 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 33/34

37 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 34/34

25 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Metacluster 2/2

Pattern 1/6

109 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 2/6

84 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 3/6

47 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 4/6

41 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 5/6

28 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)

Pattern 6/6

24 seqlets

Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)
In [12]:
run_and_plot_tomtom(modisco_out_path, motif_pfms, motif_hcwms, motif_pfms_short, num_metaclusters)

Metacluster 1/2

The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco/tomtom' already exists.
Its contents will be overwritten.
Processing query 1 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.972668
Processing query 2 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.9855
Processing query 3 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.985757
Processing query 4 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.957616
Processing query 5 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 6 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.996804
Processing query 7 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.993429
Processing query 8 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.998859
Processing query 9 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.969023
Processing query 10 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.989097
Processing query 11 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 12 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 13 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.97084
Processing query 14 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.995476
Processing query 15 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 16 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.98076
Processing query 17 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.946735
Processing query 18 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.966958
Processing query 19 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.970059
Processing query 20 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.974796
Processing query 21 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.977279
Processing query 22 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.999515
Processing query 23 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.966675
Processing query 24 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.950242
Processing query 25 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.983756
Processing query 26 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.998346
Processing query 27 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.94489
Processing query 28 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 29 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.997318
Processing query 30 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 31 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.998089
Processing query 32 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.976301
Processing query 33 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.963545
Processing query 34 out of 34 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Can't locate HtmlMonolithWr.pm:   /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48.
Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.

Motif 1/34

Motif IDq-valPWM
MA0741.1-KLF160.00025475
MA0685.2-SP40.00025475
MA0742.2-KLF120.00025475
MA0516.3-SP20.000261948
MA1511.2-KLF100.000261948

Motif 2/34

Motif IDq-valPWM
MA0764.3-ETV44.47481e-05
MA0076.2-ELK44.47481e-05
MA0916.1-Ets21C4.71171e-05
MA1854.1-Etv1/4/57.27157e-05
MA0759.2-ELK30.000113081

Motif 3/34

Motif IDq-valPWM
MA0489.2-Jun7.75468e-05
MA1988.1-Atf39.3236e-05
MA1928.1-BNC29.3236e-05
MA0591.1-Bach1::Mafk0.0003931
MA0099.3-FOS::JUN0.0003931

Motif 4/34

Motif IDq-valPWM
MA0588.1-TGA10.00460754
MA1129.1-FOSL1::JUN0.00460754
MA0831.3-TFE30.00460754
MA0609.2-CREM0.00460754
MA1131.1-FOSL2::JUN0.00460754

Motif 5/34

Motif IDq-valPWM
MA0060.3-NFYA1.1169e-05
MA1644.1-NFYC1.1169e-05
MA0314.2-HAP31.1169e-05
MA0502.2-NFYB0.0098343
MA0316.1-HAP50.0103072

Motif 6/34

Motif IDq-valPWM
MA1651.1-ZFP420.00336629
MA0748.2-YY20.00532593
MA0095.3-Yy10.0451474
MA1927.1-YY1-20.0451474
MA1460.1-pho0.0757862

Motif 7/34

Motif IDq-valPWM
MA0833.2-ATF42.71858e-06
MA1636.1-CEBPG9.13744e-05
MA1702.1-Pdp10.0682883
MA0025.2-NFIL30.0682883
MA0488.1-JUN0.0912031

Motif 8/34

Motif IDq-valPWM
MA0506.2-Nrf10.000542228
MA1412.1-TSAR20.462242

Motif 9/34

Motif IDq-valPWM
MA1034.1-Os05g04972000.00212664
MA1818.1-Zm00001d0522290.00212664
MA1819.1-Zm00001d0058920.00212664
MA1832.1-Zm00001d0023640.00212664
MA0997.1-ERF0690.00212664

Motif 10/34

Motif IDq-valPWM
MA0474.3-Erg2.28405e-06
MA0062.3-GABPA2.28405e-06
MA0473.3-ELF15.80906e-06
MA0761.2-ETV15.80906e-06
MA0598.3-EHF5.80906e-06

Motif 11/34

Motif IDq-valPWM
MA1573.2-Thap111.00021e-07
MA0088.2-ZNF1430.00794654
MA1716.1-ZNF760.0161486
MA1625.1-Stat5b0.115358
MA0519.1-Stat5a::Stat5b0.168547

Motif 12/34

Motif IDq-valPWM
MA0506.2-Nrf10.0758358

Motif 13/34

Motif IDq-valPWM
MA0139.1-CTCF6.08737e-08
MA1929.1-CTCF3.56838e-06
MA1930.1-CTCF2.18475e-05
MA1102.2-CTCFL2.18475e-05
MA0531.1-CTCF3.12418e-05

Motif 14/34

Motif IDq-valPWM
MA0361.1-RDS10.0288135
MA0429.1-YLL054C0.0288135
MA0544.1-snpc-40.42518

Motif 15/34

Motif IDq-valPWM
MA0527.1-ZBTB331.68083e-07

Motif 16/34

Motif IDq-valPWM
MA0506.2-Nrf10.127445
MA1817.1-Zm00001d0202670.127445
MA1826.1-bHLH1450.127445
MA1820.1-Zm00001d0243240.127445
MA0979.1-ERF0080.127445

Motif 17/34

Motif IDq-valPWM
MA0506.2-Nrf10.0534958
MA1650.1-ZBTB140.0534958
MA1818.1-Zm00001d0522290.0534958
MA2022.1-LOB0.0534958
MA1266.1-RAP2-110.0534958

Motif 18/34

Motif IDq-valPWM
MA1833.1-Zm00001d0493640.00172652
MA1817.1-Zm00001d0202670.00589692
MA1228.1-ERF0910.00589692
MA2013.1-ERF1150.00910219
MA1671.1-ERF1180.00910219

Motif 19/34

Motif IDq-valPWM
MA0374.1-RSC30.03013
MA1818.1-Zm00001d0522290.0556004
MA0531.1-CTCF0.0556004
MA1832.1-Zm00001d0023640.0556004
MA1821.1-Zm00001d0205950.0556004

Motif 20/34

Motif IDq-valPWM
MA1650.1-ZBTB140.242276
MA0394.1-STP10.242276
MA0399.1-SUT10.242276
MA0320.1-IME10.242276
MA1004.1-ERF130.242276

Motif 21/34

Motif IDq-valPWM
MA1833.1-Zm00001d0493640.00266617
MA1228.1-ERF0910.00266617
MA1053.1-ERF1090.00266617
MA1257.1-ERF90.00266617
MA1262.1-ERF20.00266617

Motif 22/34

No TOMTOM matches passing threshold

Motif 23/34

Motif IDq-valPWM
MA0506.2-Nrf10.000474553
MA1650.1-ZBTB140.00121867
MA0374.1-RSC30.00495054
MA1826.1-bHLH1450.00701872
MA0399.1-SUT10.0152841

Motif 24/34

Motif IDq-valPWM
MA1833.1-Zm00001d0493640.00151446
MA0506.2-Nrf10.00231364
MA1239.1-ERF1040.00231364
MA2022.1-LOB0.00231364
MA1246.1-LEP0.00231364

Motif 25/34

Motif IDq-valPWM
MA1006.1-ERF60.426275
MA1728.1-ZNF5490.426275
MA1878.1-Hes-c0.426275
MA1854.1-Etv1/4/50.426275
MA0399.1-SUT10.426275

Motif 26/34

Motif IDq-valPWM
MA0836.2-CEBPD0.000339892
MA0102.4-CEBPA0.00050521
MA0837.2-CEBPE0.00292024
MA0466.3-CEBPB0.00292024
MA1702.1-Pdp10.00798822

Motif 27/34

Motif IDq-valPWM
MA1833.1-Zm00001d0493645.30301e-06
MA1817.1-Zm00001d0202671.95309e-05
MA1819.1-Zm00001d0058921.95309e-05
MA1820.1-Zm00001d0243242.01619e-05
MA2022.1-LOB5.0344e-05

Motif 28/34

Motif IDq-valPWM
MA1573.2-Thap115.14287e-05
MA1687.1-ARF140.268811

Motif 29/34

Motif IDq-valPWM
MA0139.1-CTCF3.14561e-12
MA1929.1-CTCF8.00842e-12
MA1930.1-CTCF1.78251e-11
MA1102.2-CTCFL0.00252869
MA0531.1-CTCF0.00770196

Motif 30/34

No TOMTOM matches passing threshold

Motif 31/34

Motif IDq-valPWM
MA0798.3-RFX33.89302e-08
MA0510.2-RFX53.89302e-08
MA0509.3-RFX13.89302e-08
MA0600.2-RFX23.89302e-08
MA0365.1-RFX10.0318262

Motif 32/34

Motif IDq-valPWM
MA1573.2-Thap110.0520477
MA1513.1-KLF150.0520477
MA1716.1-ZNF760.065572
MA1687.1-ARF140.065572
MA1285.1-TCP90.065572

Motif 33/34

Motif IDq-valPWM
MA1513.1-KLF150.000201701
MA0685.2-SP40.000317601
MA0742.2-KLF120.000317601
MA1511.2-KLF100.000317601
MA1890.1-Klf150.000317601

Motif 34/34

Motif IDq-valPWM
MA0139.1-CTCF1.58201e-05
MA1929.1-CTCF0.00385279
MA0531.1-CTCF0.00385279
MA1930.1-CTCF0.00385279
MA1102.2-CTCFL0.0547218

Metacluster 2/2

The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco/tomtom' already exists.
Its contents will be overwritten.
Processing query 1 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.953111
Processing query 2 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.948677
Processing query 3 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 4 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=0.997318
Processing query 5 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Processing query 6 out of 6 
Estimating pi_0 from all 3912 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Can't locate HtmlMonolithWr.pm:   /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48.
Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.

Motif 1/6

Motif IDq-valPWM
MA1890.1-Klf150.0050389
MA1892.1-Klf5-like0.00678531
MA1410.1-StBRC10.00678531
MA1961.1-PATZ10.0114908
MA1817.1-Zm00001d0202670.0119187

Motif 2/6

Motif IDq-valPWM
MA1833.1-Zm00001d0493640.0146857
MA1712.1-ZNF4540.0146857
MA1880.1-Hey0.0146857
MA1820.1-Zm00001d0243240.0146857
MA0163.1-PLAG10.0146857

Motif 3/6

No TOMTOM matches passing threshold

Motif 4/6

No TOMTOM matches passing threshold

Motif 5/6

No TOMTOM matches passing threshold

Motif 6/6

No TOMTOM matches passing threshold