Job ID = 6367901 SRX = SRX4194193 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:48:36 prefetch.2.10.7: 1) Downloading 'SRR7291462'... 2020-06-15T23:48:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:36 prefetch.2.10.7: 'SRR7291462' is valid 2020-06-15T23:49:36 prefetch.2.10.7: 1) 'SRR7291462' was downloaded successfully 2020-06-15T23:49:36 prefetch.2.10.7: 'SRR7291462' has 0 unresolved dependencies Read 5767727 spots for SRR7291462/SRR7291462.sra Written 5767727 spots for SRR7291462/SRR7291462.sra 2020-06-15T23:50:10 prefetch.2.10.7: 1) Downloading 'SRR7291463'... 2020-06-15T23:50:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:03 prefetch.2.10.7: 'SRR7291463' is valid 2020-06-15T23:51:03 prefetch.2.10.7: 1) 'SRR7291463' was downloaded successfully 2020-06-15T23:51:03 prefetch.2.10.7: 'SRR7291463' has 0 unresolved dependencies Read 5628088 spots for SRR7291463/SRR7291463.sra Written 5628088 spots for SRR7291463/SRR7291463.sra 2020-06-15T23:51:33 prefetch.2.10.7: 1) Downloading 'SRR7291464'... 2020-06-15T23:51:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:51 prefetch.2.10.7: 'SRR7291464' is valid 2020-06-15T23:52:51 prefetch.2.10.7: 1) 'SRR7291464' was downloaded successfully 2020-06-15T23:52:51 prefetch.2.10.7: 'SRR7291464' has 0 unresolved dependencies Read 5766137 spots for SRR7291464/SRR7291464.sra Written 5766137 spots for SRR7291464/SRR7291464.sra 2020-06-15T23:53:22 prefetch.2.10.7: 1) Downloading 'SRR7291465'... 2020-06-15T23:53:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:12 prefetch.2.10.7: 'SRR7291465' is valid 2020-06-15T23:54:12 prefetch.2.10.7: 1) 'SRR7291465' was downloaded successfully 2020-06-15T23:54:12 prefetch.2.10.7: 'SRR7291465' has 0 unresolved dependencies Read 5566012 spots for SRR7291465/SRR7291465.sra Written 5566012 spots for SRR7291465/SRR7291465.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:22 22727964 reads; of these: 22727964 (100.00%) were unpaired; of these: 528053 (2.32%) aligned 0 times 17961018 (79.03%) aligned exactly 1 time 4238893 (18.65%) aligned >1 times 97.68% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 5774529 / 22199911 = 0.2601 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 09:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.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 09:09:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:52: 1000000 INFO @ Tue, 16 Jun 2020 09:09:59: 2000000 INFO @ Tue, 16 Jun 2020 09:10:05: 3000000 INFO @ Tue, 16 Jun 2020 09:10:12: 4000000 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 09:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.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 09:10:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:19: 5000000 INFO @ Tue, 16 Jun 2020 09:10:22: 1000000 INFO @ Tue, 16 Jun 2020 09:10:27: 6000000 INFO @ Tue, 16 Jun 2020 09:10:30: 2000000 INFO @ Tue, 16 Jun 2020 09:10:34: 7000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 INFO @ Tue, 16 Jun 2020 09:10:42: 8000000 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 09:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.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 09:10:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:45: 4000000 INFO @ Tue, 16 Jun 2020 09:10:49: 9000000 INFO @ Tue, 16 Jun 2020 09:10:52: 1000000 INFO @ Tue, 16 Jun 2020 09:10:53: 5000000 INFO @ Tue, 16 Jun 2020 09:10:57: 10000000 INFO @ Tue, 16 Jun 2020 09:11:00: 2000000 INFO @ Tue, 16 Jun 2020 09:11:01: 6000000 INFO @ Tue, 16 Jun 2020 09:11:05: 11000000 INFO @ Tue, 16 Jun 2020 09:11:08: 3000000 INFO @ Tue, 16 Jun 2020 09:11:09: 7000000 INFO @ Tue, 16 Jun 2020 09:11:12: 12000000 INFO @ Tue, 16 Jun 2020 09:11:15: 4000000 INFO @ Tue, 16 Jun 2020 09:11:16: 8000000 INFO @ Tue, 16 Jun 2020 09:11:20: 13000000 INFO @ Tue, 16 Jun 2020 09:11:23: 5000000 INFO @ Tue, 16 Jun 2020 09:11:24: 9000000 INFO @ Tue, 16 Jun 2020 09:11:28: 14000000 INFO @ Tue, 16 Jun 2020 09:11:31: 6000000 INFO @ Tue, 16 Jun 2020 09:11:32: 10000000 INFO @ Tue, 16 Jun 2020 09:11:36: 15000000 INFO @ Tue, 16 Jun 2020 09:11:39: 7000000 INFO @ Tue, 16 Jun 2020 09:11:40: 11000000 INFO @ Tue, 16 Jun 2020 09:11:44: 16000000 INFO @ Tue, 16 Jun 2020 09:11:47: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:11:47: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:11:47: #1 total tags in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:11:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:47: #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 09:11:47: #1 tags after filtering in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:48: 8000000 INFO @ Tue, 16 Jun 2020 09:11:48: 12000000 INFO @ Tue, 16 Jun 2020 09:11:49: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 09:11:49: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:49: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:11:49: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:49: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:11:49: #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 09:11:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:56: 9000000 INFO @ Tue, 16 Jun 2020 09:11:56: 13000000 INFO @ Tue, 16 Jun 2020 09:12:04: 14000000 INFO @ Tue, 16 Jun 2020 09:12:04: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:12: 15000000 INFO @ Tue, 16 Jun 2020 09:12:12: 11000000 INFO @ Tue, 16 Jun 2020 09:12:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:20: 16000000 INFO @ Tue, 16 Jun 2020 09:12:20: 12000000 INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:12:23: #1 total tags in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:12:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:23: #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 09:12:23: #1 tags after filtering in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 09:12:24: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:24: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:27: 13000000 INFO @ Tue, 16 Jun 2020 09:12:34: 14000000 INFO @ Tue, 16 Jun 2020 09:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:41: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:48: 16000000 INFO @ Tue, 16 Jun 2020 09:12:51: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:12:51: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:12:51: #1 total tags in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:12:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:51: #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 09:12:51: #1 tags after filtering in treatment: 16425382 INFO @ Tue, 16 Jun 2020 09:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:52: #2 number of paired peaks: 370 WARNING @ Tue, 16 Jun 2020 09:12:52: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:12:52: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 09:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:52: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 09:12:52: #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 09:12:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (445 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194193/SRX4194193.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling