Job ID = 16435031 SRX = SRX13110320 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:33:02 prefetch.2.10.7: 1) Downloading 'SRR16917990'... 2022-08-02T01:33:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:33:30 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:33:31 prefetch.2.10.7: 'SRR16917990' is valid 2022-08-02T01:33:31 prefetch.2.10.7: 1) 'SRR16917990' was downloaded successfully 2022-08-02T01:33:31 prefetch.2.10.7: 'SRR16917990' has 0 unresolved dependencies Read 16561614 spots for SRR16917990/SRR16917990.sra Written 16561614 spots for SRR16917990/SRR16917990.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435504 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:53 16561614 reads; of these: 16561614 (100.00%) were unpaired; of these: 1883811 (11.37%) aligned 0 times 12494859 (75.44%) aligned exactly 1 time 2182944 (13.18%) aligned >1 times 88.63% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 1650061 / 14677803 = 0.1124 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:43:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.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, 02 Aug 2022 10:43:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:10: 1000000 INFO @ Tue, 02 Aug 2022 10:43:16: 2000000 INFO @ Tue, 02 Aug 2022 10:43:23: 3000000 INFO @ Tue, 02 Aug 2022 10:43:29: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.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, 02 Aug 2022 10:43:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:35: 5000000 INFO @ Tue, 02 Aug 2022 10:43:39: 1000000 INFO @ Tue, 02 Aug 2022 10:43:42: 6000000 INFO @ Tue, 02 Aug 2022 10:43:46: 2000000 INFO @ Tue, 02 Aug 2022 10:43:49: 7000000 INFO @ Tue, 02 Aug 2022 10:43:53: 3000000 INFO @ Tue, 02 Aug 2022 10:43:56: 8000000 INFO @ Tue, 02 Aug 2022 10:44:00: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.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, 02 Aug 2022 10:44:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:44:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:44:03: 9000000 INFO @ Tue, 02 Aug 2022 10:44:07: 5000000 INFO @ Tue, 02 Aug 2022 10:44:10: 10000000 INFO @ Tue, 02 Aug 2022 10:44:11: 1000000 INFO @ Tue, 02 Aug 2022 10:44:15: 6000000 INFO @ Tue, 02 Aug 2022 10:44:18: 11000000 INFO @ Tue, 02 Aug 2022 10:44:18: 2000000 INFO @ Tue, 02 Aug 2022 10:44:22: 7000000 INFO @ Tue, 02 Aug 2022 10:44:26: 12000000 INFO @ Tue, 02 Aug 2022 10:44:26: 3000000 INFO @ Tue, 02 Aug 2022 10:44:30: 8000000 INFO @ Tue, 02 Aug 2022 10:44:33: 13000000 INFO @ Tue, 02 Aug 2022 10:44:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:44:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:44:33: #1 total tags in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:44:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:44:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:44:34: #1 tags after filtering in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:44:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:44:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:44:34: 4000000 INFO @ Tue, 02 Aug 2022 10:44:34: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:44:34: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:44:34: start model_add_line... INFO @ Tue, 02 Aug 2022 10:44:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:44:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:44:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:44:35: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:44:35: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05_model.r WARNING @ Tue, 02 Aug 2022 10:44:35: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:44:35: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:44:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:44:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:44:37: 9000000 INFO @ Tue, 02 Aug 2022 10:44:42: 5000000 INFO @ Tue, 02 Aug 2022 10:44:45: 10000000 INFO @ Tue, 02 Aug 2022 10:44:50: 6000000 INFO @ Tue, 02 Aug 2022 10:44:52: 11000000 INFO @ Tue, 02 Aug 2022 10:44:58: 7000000 INFO @ Tue, 02 Aug 2022 10:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:44:59: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:45:06: 8000000 INFO @ Tue, 02 Aug 2022 10:45:06: 13000000 INFO @ Tue, 02 Aug 2022 10:45:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:45:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:45:07: #1 total tags in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:45:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:45:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:45:07: #1 tags after filtering in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:45:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:45:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:45:08: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:45:08: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:45:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:45:08: start X-correlation... INFO @ Tue, 02 Aug 2022 10:45:08: end of X-cor INFO @ Tue, 02 Aug 2022 10:45:08: #2 finished! INFO @ Tue, 02 Aug 2022 10:45:08: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:45:08: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10_model.r WARNING @ Tue, 02 Aug 2022 10:45:08: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:45:08: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:45:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:45:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.05_summits.bed INFO @ Tue, 02 Aug 2022 10:45:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1445 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:45:13: 9000000 INFO @ Tue, 02 Aug 2022 10:45:20: 10000000 INFO @ Tue, 02 Aug 2022 10:45:26: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:45:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:45:33: 12000000 INFO @ Tue, 02 Aug 2022 10:45:39: 13000000 INFO @ Tue, 02 Aug 2022 10:45:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:45:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:45:39: #1 total tags in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:45:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:45:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:45:39: #1 tags after filtering in treatment: 13027742 INFO @ Tue, 02 Aug 2022 10:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:45:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:45:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:45:40: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:45:40: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:45:40: start model_add_line... INFO @ Tue, 02 Aug 2022 10:45:40: start X-correlation... INFO @ Tue, 02 Aug 2022 10:45:40: end of X-cor INFO @ Tue, 02 Aug 2022 10:45:40: #2 finished! INFO @ Tue, 02 Aug 2022 10:45:40: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:45:40: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20_model.r WARNING @ Tue, 02 Aug 2022 10:45:40: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:45:40: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:45:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:45:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.10_summits.bed INFO @ Tue, 02 Aug 2022 10:45:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (758 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:46:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:46:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:46:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:46:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110320/SRX13110320.20_summits.bed INFO @ Tue, 02 Aug 2022 10:46:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 14 millis CompletedMACS2peakCalling