Job ID = 6367207 SRX = SRX2985927 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:46 prefetch.2.10.7: 1) Downloading 'SRR5807077'... 2020-06-15T23:21:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:50 prefetch.2.10.7: 1) 'SRR5807077' was downloaded successfully 2020-06-15T23:23:50 prefetch.2.10.7: 'SRR5807077' has 0 unresolved dependencies Read 45543277 spots for SRR5807077/SRR5807077.sra Written 45543277 spots for SRR5807077/SRR5807077.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: 00:10:52 45543277 reads; of these: 45543277 (100.00%) were unpaired; of these: 1662043 (3.65%) aligned 0 times 33618843 (73.82%) aligned exactly 1 time 10262391 (22.53%) aligned >1 times 96.35% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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 20 files... [bam_rmdupse_core] 23579457 / 43881234 = 0.5373 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 08:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.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 08:43:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:34: 1000000 INFO @ Tue, 16 Jun 2020 08:43:39: 2000000 INFO @ Tue, 16 Jun 2020 08:43:44: 3000000 INFO @ Tue, 16 Jun 2020 08:43:49: 4000000 INFO @ Tue, 16 Jun 2020 08:43:54: 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 08:43:58: 6000000 INFO @ Tue, 16 Jun 2020 08:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.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 08:43:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:04: 7000000 INFO @ Tue, 16 Jun 2020 08:44:04: 1000000 INFO @ Tue, 16 Jun 2020 08:44:09: 8000000 INFO @ Tue, 16 Jun 2020 08:44:09: 2000000 INFO @ Tue, 16 Jun 2020 08:44:14: 9000000 INFO @ Tue, 16 Jun 2020 08:44:14: 3000000 INFO @ Tue, 16 Jun 2020 08:44:19: 10000000 INFO @ Tue, 16 Jun 2020 08:44:19: 4000000 INFO @ Tue, 16 Jun 2020 08:44:24: 11000000 INFO @ Tue, 16 Jun 2020 08:44:24: 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 08:44:29: 12000000 INFO @ Tue, 16 Jun 2020 08:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.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 08:44:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:29: 6000000 INFO @ Tue, 16 Jun 2020 08:44:34: 13000000 INFO @ Tue, 16 Jun 2020 08:44:34: 1000000 INFO @ Tue, 16 Jun 2020 08:44:35: 7000000 INFO @ Tue, 16 Jun 2020 08:44:39: 14000000 INFO @ Tue, 16 Jun 2020 08:44:39: 2000000 INFO @ Tue, 16 Jun 2020 08:44:40: 8000000 INFO @ Tue, 16 Jun 2020 08:44:44: 15000000 INFO @ Tue, 16 Jun 2020 08:44:44: 3000000 INFO @ Tue, 16 Jun 2020 08:44:45: 9000000 INFO @ Tue, 16 Jun 2020 08:44:49: 16000000 INFO @ Tue, 16 Jun 2020 08:44:49: 4000000 INFO @ Tue, 16 Jun 2020 08:44:50: 10000000 INFO @ Tue, 16 Jun 2020 08:44:54: 17000000 INFO @ Tue, 16 Jun 2020 08:44:54: 5000000 INFO @ Tue, 16 Jun 2020 08:44:55: 11000000 INFO @ Tue, 16 Jun 2020 08:44:59: 18000000 INFO @ Tue, 16 Jun 2020 08:44:59: 6000000 INFO @ Tue, 16 Jun 2020 08:45:00: 12000000 INFO @ Tue, 16 Jun 2020 08:45:04: 19000000 INFO @ Tue, 16 Jun 2020 08:45:04: 7000000 INFO @ Tue, 16 Jun 2020 08:45:05: 13000000 INFO @ Tue, 16 Jun 2020 08:45:09: 20000000 INFO @ Tue, 16 Jun 2020 08:45:09: 8000000 INFO @ Tue, 16 Jun 2020 08:45:10: 14000000 INFO @ Tue, 16 Jun 2020 08:45:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:45:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:45:11: #1 total tags in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:45:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:11: #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 08:45:11: #1 tags after filtering in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:13: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:45:13: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:13: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:45:13: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Tue, 16 Jun 2020 08:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05_model.r WARNING @ Tue, 16 Jun 2020 08:45:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:13: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Tue, 16 Jun 2020 08:45:13: #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 08:45:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:14: 9000000 INFO @ Tue, 16 Jun 2020 08:45:15: 15000000 INFO @ Tue, 16 Jun 2020 08:45:19: 10000000 INFO @ Tue, 16 Jun 2020 08:45:20: 16000000 INFO @ Tue, 16 Jun 2020 08:45:24: 11000000 INFO @ Tue, 16 Jun 2020 08:45:25: 17000000 INFO @ Tue, 16 Jun 2020 08:45:29: 12000000 INFO @ Tue, 16 Jun 2020 08:45:30: 18000000 INFO @ Tue, 16 Jun 2020 08:45:34: 13000000 INFO @ Tue, 16 Jun 2020 08:45:34: 19000000 INFO @ Tue, 16 Jun 2020 08:45:39: 14000000 INFO @ Tue, 16 Jun 2020 08:45:39: 20000000 INFO @ Tue, 16 Jun 2020 08:45:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:45:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:45:41: #1 total tags in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:45:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:41: #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 08:45:41: #1 tags after filtering in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:43: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:45:43: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:45:43: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Tue, 16 Jun 2020 08:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:43: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Tue, 16 Jun 2020 08:45:43: #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 08:45:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:43: 15000000 INFO @ Tue, 16 Jun 2020 08:45:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:48: 16000000 INFO @ Tue, 16 Jun 2020 08:45:53: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:58: 18000000 INFO @ Tue, 16 Jun 2020 08:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:00: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:03: 19000000 INFO @ Tue, 16 Jun 2020 08:46:07: 20000000 INFO @ Tue, 16 Jun 2020 08:46:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:46:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:46:09: #1 total tags in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:46:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:09: #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 08:46:09: #1 tags after filtering in treatment: 20301777 INFO @ Tue, 16 Jun 2020 08:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:11: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:46:11: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:46:11: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Tue, 16 Jun 2020 08:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20_model.r WARNING @ Tue, 16 Jun 2020 08:46:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:11: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Tue, 16 Jun 2020 08:46:11: #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 08:46:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2985927/SRX2985927.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling