Job ID = 6368659 SRX = SRX529219 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:48 prefetch.2.10.7: 1) Downloading 'SRR1265823'... 2020-06-16T00:22:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:47 prefetch.2.10.7: 1) 'SRR1265823' was downloaded successfully Read 29041160 spots for SRR1265823/SRR1265823.sra Written 29041160 spots for SRR1265823/SRR1265823.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: 00:03:47 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10749453 (37.01%) aligned 0 times 15214300 (52.39%) aligned exactly 1 time 3077407 (10.60%) aligned >1 times 62.99% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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 8 files... [bam_rmdupse_core] 1906493 / 18291707 = 0.1042 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 09:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.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 09:35:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:22: 1000000 INFO @ Tue, 16 Jun 2020 09:35:27: 2000000 INFO @ Tue, 16 Jun 2020 09:35:33: 3000000 INFO @ Tue, 16 Jun 2020 09:35:38: 4000000 INFO @ Tue, 16 Jun 2020 09:35:43: 5000000 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 09:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.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 09:35:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:49: 6000000 INFO @ Tue, 16 Jun 2020 09:35:52: 1000000 INFO @ Tue, 16 Jun 2020 09:35:54: 7000000 INFO @ Tue, 16 Jun 2020 09:35:57: 2000000 INFO @ Tue, 16 Jun 2020 09:36:00: 8000000 INFO @ Tue, 16 Jun 2020 09:36:03: 3000000 INFO @ Tue, 16 Jun 2020 09:36:05: 9000000 INFO @ Tue, 16 Jun 2020 09:36:08: 4000000 INFO @ Tue, 16 Jun 2020 09:36:11: 10000000 INFO @ Tue, 16 Jun 2020 09:36:13: 5000000 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 09:36:16: 11000000 INFO @ Tue, 16 Jun 2020 09:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.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 09:36:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:19: 6000000 INFO @ Tue, 16 Jun 2020 09:36:21: 12000000 INFO @ Tue, 16 Jun 2020 09:36:22: 1000000 INFO @ Tue, 16 Jun 2020 09:36:24: 7000000 INFO @ Tue, 16 Jun 2020 09:36:27: 13000000 INFO @ Tue, 16 Jun 2020 09:36:28: 2000000 INFO @ Tue, 16 Jun 2020 09:36:30: 8000000 INFO @ Tue, 16 Jun 2020 09:36:32: 14000000 INFO @ Tue, 16 Jun 2020 09:36:34: 3000000 INFO @ Tue, 16 Jun 2020 09:36:36: 9000000 INFO @ Tue, 16 Jun 2020 09:36:38: 15000000 INFO @ Tue, 16 Jun 2020 09:36:39: 4000000 INFO @ Tue, 16 Jun 2020 09:36:41: 10000000 INFO @ Tue, 16 Jun 2020 09:36:43: 16000000 INFO @ Tue, 16 Jun 2020 09:36:45: 5000000 INFO @ Tue, 16 Jun 2020 09:36:45: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:36:45: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:36:45: #1 total tags in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:36:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:45: #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 09:36:46: #1 tags after filtering in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:47: #2 number of paired peaks: 224 WARNING @ Tue, 16 Jun 2020 09:36:47: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:47: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 09:36:47: #2 alternative fragment length(s) may be 1,30,562 bps INFO @ Tue, 16 Jun 2020 09:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:47: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:47: #2 You may need to consider one of the other alternative d(s): 1,30,562 WARNING @ Tue, 16 Jun 2020 09:36:47: #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 09:36:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:47: 11000000 INFO @ Tue, 16 Jun 2020 09:36:51: 6000000 INFO @ Tue, 16 Jun 2020 09:36:53: 12000000 INFO @ Tue, 16 Jun 2020 09:36:56: 7000000 INFO @ Tue, 16 Jun 2020 09:36:58: 13000000 INFO @ Tue, 16 Jun 2020 09:37:02: 8000000 INFO @ Tue, 16 Jun 2020 09:37:04: 14000000 INFO @ Tue, 16 Jun 2020 09:37:08: 9000000 INFO @ Tue, 16 Jun 2020 09:37:10: 15000000 INFO @ Tue, 16 Jun 2020 09:37:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:13: 10000000 INFO @ Tue, 16 Jun 2020 09:37:15: 16000000 INFO @ Tue, 16 Jun 2020 09:37:17: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:37:17: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:37:17: #1 total tags in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:37:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:17: #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 09:37:18: #1 tags after filtering in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:37:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:19: 11000000 INFO @ Tue, 16 Jun 2020 09:37:19: #2 number of paired peaks: 224 WARNING @ Tue, 16 Jun 2020 09:37:19: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:19: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 09:37:19: #2 alternative fragment length(s) may be 1,30,562 bps INFO @ Tue, 16 Jun 2020 09:37:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:19: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:19: #2 You may need to consider one of the other alternative d(s): 1,30,562 WARNING @ Tue, 16 Jun 2020 09:37:19: #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 09:37:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:24: 12000000 INFO @ Tue, 16 Jun 2020 09:37:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:29: 13000000 INFO @ Tue, 16 Jun 2020 09:37:34: 14000000 INFO @ Tue, 16 Jun 2020 09:37:39: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:44: 16000000 INFO @ Tue, 16 Jun 2020 09:37:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:47: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:37:47: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:37:47: #1 total tags in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:37:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:47: #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 09:37:47: #1 tags after filtering in treatment: 16385214 INFO @ Tue, 16 Jun 2020 09:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #2 number of paired peaks: 224 WARNING @ Tue, 16 Jun 2020 09:37:48: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:48: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2 alternative fragment length(s) may be 1,30,562 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:48: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:48: #2 You may need to consider one of the other alternative d(s): 1,30,562 WARNING @ Tue, 16 Jun 2020 09:37:48: #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 09:37:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529219/SRX529219.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。