Job ID = 16434975 SRX = SRX10435540 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23290698 spots for SRR14060956/SRR14060956.sra Written 23290698 spots for SRR14060956/SRR14060956.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435132 ("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: 00:08:21 23290698 reads; of these: 23290698 (100.00%) were unpaired; of these: 475560 (2.04%) aligned 0 times 19041323 (81.76%) aligned exactly 1 time 3773815 (16.20%) aligned >1 times 97.96% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 2520453 / 22815138 = 0.1105 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 10:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.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 10:41:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:16: 1000000 INFO @ Tue, 02 Aug 2022 10:41:25: 2000000 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 10:41:35: 3000000 INFO @ Tue, 02 Aug 2022 10:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.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 10:41:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:41:43: 4000000 INFO @ Tue, 02 Aug 2022 10:41:46: 1000000 INFO @ Tue, 02 Aug 2022 10:41:52: 5000000 INFO @ Tue, 02 Aug 2022 10:41:56: 2000000 INFO @ Tue, 02 Aug 2022 10:42:01: 6000000 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 10:42:06: 3000000 INFO @ Tue, 02 Aug 2022 10:42:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.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 10:42:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:42:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:42:09: 7000000 INFO @ Tue, 02 Aug 2022 10:42:16: 4000000 INFO @ Tue, 02 Aug 2022 10:42:18: 1000000 INFO @ Tue, 02 Aug 2022 10:42:18: 8000000 INFO @ Tue, 02 Aug 2022 10:42:27: 5000000 INFO @ Tue, 02 Aug 2022 10:42:28: 9000000 INFO @ Tue, 02 Aug 2022 10:42:28: 2000000 INFO @ Tue, 02 Aug 2022 10:42:37: 10000000 INFO @ Tue, 02 Aug 2022 10:42:38: 6000000 INFO @ Tue, 02 Aug 2022 10:42:39: 3000000 INFO @ Tue, 02 Aug 2022 10:42:46: 11000000 INFO @ Tue, 02 Aug 2022 10:42:48: 7000000 INFO @ Tue, 02 Aug 2022 10:42:49: 4000000 INFO @ Tue, 02 Aug 2022 10:42:55: 12000000 INFO @ Tue, 02 Aug 2022 10:42:59: 8000000 INFO @ Tue, 02 Aug 2022 10:43:00: 5000000 INFO @ Tue, 02 Aug 2022 10:43:04: 13000000 INFO @ Tue, 02 Aug 2022 10:43:09: 9000000 INFO @ Tue, 02 Aug 2022 10:43:11: 6000000 INFO @ Tue, 02 Aug 2022 10:43:12: 14000000 INFO @ Tue, 02 Aug 2022 10:43:20: 10000000 INFO @ Tue, 02 Aug 2022 10:43:21: 7000000 INFO @ Tue, 02 Aug 2022 10:43:21: 15000000 INFO @ Tue, 02 Aug 2022 10:43:30: 16000000 INFO @ Tue, 02 Aug 2022 10:43:31: 11000000 INFO @ Tue, 02 Aug 2022 10:43:32: 8000000 INFO @ Tue, 02 Aug 2022 10:43:39: 17000000 INFO @ Tue, 02 Aug 2022 10:43:42: 12000000 INFO @ Tue, 02 Aug 2022 10:43:43: 9000000 INFO @ Tue, 02 Aug 2022 10:43:47: 18000000 INFO @ Tue, 02 Aug 2022 10:43:52: 13000000 INFO @ Tue, 02 Aug 2022 10:43:53: 10000000 INFO @ Tue, 02 Aug 2022 10:43:56: 19000000 INFO @ Tue, 02 Aug 2022 10:44:03: 14000000 INFO @ Tue, 02 Aug 2022 10:44:03: 11000000 INFO @ Tue, 02 Aug 2022 10:44:04: 20000000 INFO @ Tue, 02 Aug 2022 10:44:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:44:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:44:07: #1 total tags in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:44:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:44:07: #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 10:44:07: #1 tags after filtering in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:44:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:44:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:44:08: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:44:08: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:44:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:44:09: start X-correlation... INFO @ Tue, 02 Aug 2022 10:44:09: end of X-cor INFO @ Tue, 02 Aug 2022 10:44:09: #2 finished! INFO @ Tue, 02 Aug 2022 10:44:09: #2 predicted fragment length is 60 bps INFO @ Tue, 02 Aug 2022 10:44:09: #2 alternative fragment length(s) may be 2,60,521,543,565,590 bps INFO @ Tue, 02 Aug 2022 10:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05_model.r WARNING @ Tue, 02 Aug 2022 10:44:09: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:44:09: #2 You may need to consider one of the other alternative d(s): 2,60,521,543,565,590 WARNING @ Tue, 02 Aug 2022 10:44:09: #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 10:44:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:44:13: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:44:14: 12000000 INFO @ Tue, 02 Aug 2022 10:44:24: 16000000 INFO @ Tue, 02 Aug 2022 10:44:25: 13000000 INFO @ Tue, 02 Aug 2022 10:44:34: 17000000 INFO @ Tue, 02 Aug 2022 10:44:35: 14000000 INFO @ Tue, 02 Aug 2022 10:44:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:44:45: 18000000 INFO @ Tue, 02 Aug 2022 10:44:46: 15000000 INFO @ Tue, 02 Aug 2022 10:44:55: 19000000 INFO @ Tue, 02 Aug 2022 10:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:44:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.05_summits.bed INFO @ Tue, 02 Aug 2022 10:44:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:44:56: 16000000 INFO @ Tue, 02 Aug 2022 10:45:06: 20000000 INFO @ Tue, 02 Aug 2022 10:45:07: 17000000 INFO @ Tue, 02 Aug 2022 10:45:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:45:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:45:09: #1 total tags in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:45:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:45:09: #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 10:45:09: #1 tags after filtering in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:45:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:45:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:45:10: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:45:10: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:45:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:45:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:45:11: end of X-cor INFO @ Tue, 02 Aug 2022 10:45:11: #2 finished! INFO @ Tue, 02 Aug 2022 10:45:11: #2 predicted fragment length is 60 bps INFO @ Tue, 02 Aug 2022 10:45:11: #2 alternative fragment length(s) may be 2,60,521,543,565,590 bps INFO @ Tue, 02 Aug 2022 10:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10_model.r WARNING @ Tue, 02 Aug 2022 10:45:11: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:45:11: #2 You may need to consider one of the other alternative d(s): 2,60,521,543,565,590 WARNING @ Tue, 02 Aug 2022 10:45:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:45:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:45:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:45:18: 18000000 INFO @ Tue, 02 Aug 2022 10:45:29: 19000000 INFO @ Tue, 02 Aug 2022 10:45:39: 20000000 INFO @ Tue, 02 Aug 2022 10:45:42: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:45:42: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:45:42: #1 total tags in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:45:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:45:42: #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 10:45:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:45:43: #1 tags after filtering in treatment: 20294685 INFO @ Tue, 02 Aug 2022 10:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:45:43: #1 finished! INFO @ Tue, 02 Aug 2022 10:45:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:45:44: #2 number of paired peaks: 198 WARNING @ Tue, 02 Aug 2022 10:45:44: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 02 Aug 2022 10:45:44: start model_add_line... INFO @ Tue, 02 Aug 2022 10:45:44: start X-correlation... INFO @ Tue, 02 Aug 2022 10:45:44: end of X-cor INFO @ Tue, 02 Aug 2022 10:45:44: #2 finished! INFO @ Tue, 02 Aug 2022 10:45:44: #2 predicted fragment length is 60 bps INFO @ Tue, 02 Aug 2022 10:45:44: #2 alternative fragment length(s) may be 2,60,521,543,565,590 bps INFO @ Tue, 02 Aug 2022 10:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20_model.r WARNING @ Tue, 02 Aug 2022 10:45:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:45:44: #2 You may need to consider one of the other alternative d(s): 2,60,521,543,565,590 WARNING @ Tue, 02 Aug 2022 10:45:44: #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 10:45:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.10_summits.bed INFO @ Tue, 02 Aug 2022 10:45:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:46:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435540/SRX10435540.20_summits.bed INFO @ Tue, 02 Aug 2022 10:46:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (196 records, 4 fields): 36 millis CompletedMACS2peakCalling