Job ID = 6367908 SRX = SRX4194201 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:00 prefetch.2.10.7: 1) Downloading 'SRR7291492'... 2020-06-15T23:43:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:18 prefetch.2.10.7: 'SRR7291492' is valid 2020-06-15T23:44:18 prefetch.2.10.7: 1) 'SRR7291492' was downloaded successfully 2020-06-15T23:44:18 prefetch.2.10.7: 'SRR7291492' has 0 unresolved dependencies Read 7007671 spots for SRR7291492/SRR7291492.sra Written 7007671 spots for SRR7291492/SRR7291492.sra 2020-06-15T23:44:55 prefetch.2.10.7: 1) Downloading 'SRR7291493'... 2020-06-15T23:44:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:21 prefetch.2.10.7: 'SRR7291493' is valid 2020-06-15T23:46:21 prefetch.2.10.7: 1) 'SRR7291493' was downloaded successfully 2020-06-15T23:46:21 prefetch.2.10.7: 'SRR7291493' has 0 unresolved dependencies Read 6861708 spots for SRR7291493/SRR7291493.sra Written 6861708 spots for SRR7291493/SRR7291493.sra 2020-06-15T23:46:55 prefetch.2.10.7: 1) Downloading 'SRR7291494'... 2020-06-15T23:46:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:44 prefetch.2.10.7: 'SRR7291494' is valid 2020-06-15T23:48:44 prefetch.2.10.7: 1) 'SRR7291494' was downloaded successfully 2020-06-15T23:48:44 prefetch.2.10.7: 'SRR7291494' has 0 unresolved dependencies Read 7003828 spots for SRR7291494/SRR7291494.sra Written 7003828 spots for SRR7291494/SRR7291494.sra 2020-06-15T23:49:23 prefetch.2.10.7: 1) Downloading 'SRR7291495'... 2020-06-15T23:49:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:15 prefetch.2.10.7: 'SRR7291495' is valid 2020-06-15T23:50:15 prefetch.2.10.7: 1) 'SRR7291495' was downloaded successfully 2020-06-15T23:50:15 prefetch.2.10.7: 'SRR7291495' has 0 unresolved dependencies Read 6773131 spots for SRR7291495/SRR7291495.sra Written 6773131 spots for SRR7291495/SRR7291495.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:42 27646338 reads; of these: 27646338 (100.00%) were unpaired; of these: 463593 (1.68%) aligned 0 times 23668772 (85.61%) aligned exactly 1 time 3513973 (12.71%) aligned >1 times 98.32% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10158128 / 27182745 = 0.3737 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:08:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:16: 1000000 INFO @ Tue, 16 Jun 2020 09:08:23: 2000000 INFO @ Tue, 16 Jun 2020 09:08:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:08:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:39: 4000000 INFO @ Tue, 16 Jun 2020 09:08:46: 1000000 INFO @ Tue, 16 Jun 2020 09:08:48: 5000000 INFO @ Tue, 16 Jun 2020 09:08:54: 2000000 INFO @ Tue, 16 Jun 2020 09:08:57: 6000000 INFO @ Tue, 16 Jun 2020 09:09:02: 3000000 INFO @ Tue, 16 Jun 2020 09:09:05: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:09:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:11: 4000000 INFO @ Tue, 16 Jun 2020 09:09:14: 8000000 INFO @ Tue, 16 Jun 2020 09:09:16: 1000000 INFO @ Tue, 16 Jun 2020 09:09:20: 5000000 INFO @ Tue, 16 Jun 2020 09:09:23: 9000000 INFO @ Tue, 16 Jun 2020 09:09:25: 2000000 INFO @ Tue, 16 Jun 2020 09:09:29: 6000000 INFO @ Tue, 16 Jun 2020 09:09:32: 10000000 INFO @ Tue, 16 Jun 2020 09:09:35: 3000000 INFO @ Tue, 16 Jun 2020 09:09:39: 7000000 INFO @ Tue, 16 Jun 2020 09:09:41: 11000000 INFO @ Tue, 16 Jun 2020 09:09:44: 4000000 INFO @ Tue, 16 Jun 2020 09:09:49: 8000000 INFO @ Tue, 16 Jun 2020 09:09:50: 12000000 INFO @ Tue, 16 Jun 2020 09:09:54: 5000000 INFO @ Tue, 16 Jun 2020 09:09:59: 13000000 INFO @ Tue, 16 Jun 2020 09:09:59: 9000000 INFO @ Tue, 16 Jun 2020 09:10:03: 6000000 INFO @ Tue, 16 Jun 2020 09:10:07: 14000000 INFO @ Tue, 16 Jun 2020 09:10:09: 10000000 INFO @ Tue, 16 Jun 2020 09:10:13: 7000000 INFO @ Tue, 16 Jun 2020 09:10:16: 15000000 INFO @ Tue, 16 Jun 2020 09:10:19: 11000000 INFO @ Tue, 16 Jun 2020 09:10:23: 8000000 INFO @ Tue, 16 Jun 2020 09:10:25: 16000000 INFO @ Tue, 16 Jun 2020 09:10:29: 12000000 INFO @ Tue, 16 Jun 2020 09:10:33: 9000000 INFO @ Tue, 16 Jun 2020 09:10:34: 17000000 INFO @ Tue, 16 Jun 2020 09:10:34: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:10:34: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:10:34: #1 total tags in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:10:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:10:34: #1 tags after filtering in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:35: #2 number of paired peaks: 170 WARNING @ Tue, 16 Jun 2020 09:10:35: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:36: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:10:36: #2 alternative fragment length(s) may be 2,61 bps INFO @ Tue, 16 Jun 2020 09:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:36: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:36: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Tue, 16 Jun 2020 09:10:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:10:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:39: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:43: 10000000 INFO @ Tue, 16 Jun 2020 09:10:48: 14000000 INFO @ Tue, 16 Jun 2020 09:10:52: 11000000 INFO @ Tue, 16 Jun 2020 09:10:57: 15000000 INFO @ Tue, 16 Jun 2020 09:11:01: 12000000 INFO @ Tue, 16 Jun 2020 09:11:07: 16000000 INFO @ Tue, 16 Jun 2020 09:11:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:10: 13000000 INFO @ Tue, 16 Jun 2020 09:11:16: 17000000 INFO @ Tue, 16 Jun 2020 09:11:16: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:11:16: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:11:16: #1 total tags in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:11:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:16: #1 tags after filtering in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:17: #2 number of paired peaks: 170 WARNING @ Tue, 16 Jun 2020 09:11:17: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:18: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:11:18: #2 alternative fragment length(s) may be 2,61 bps INFO @ Tue, 16 Jun 2020 09:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:18: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Tue, 16 Jun 2020 09:11:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:11:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:19: 14000000 INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3334 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:27: 15000000 INFO @ Tue, 16 Jun 2020 09:11:36: 16000000 INFO @ Tue, 16 Jun 2020 09:11:44: 17000000 INFO @ Tue, 16 Jun 2020 09:11:44: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:11:44: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:11:44: #1 total tags in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:11:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:44: #1 tags after filtering in treatment: 17024617 INFO @ Tue, 16 Jun 2020 09:11:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:45: #2 number of paired peaks: 170 WARNING @ Tue, 16 Jun 2020 09:11:45: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:46: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:11:46: #2 alternative fragment length(s) may be 2,61 bps INFO @ Tue, 16 Jun 2020 09:11:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:46: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:46: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Tue, 16 Jun 2020 09:11:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:11:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194201/SRX4194201.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling