Job ID = 16439489 SRX = SRX13227899 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:12:30 35987896 reads; of these: 35987896 (100.00%) were unpaired; of these: 6608973 (18.36%) aligned 0 times 22499555 (62.52%) aligned exactly 1 time 6879368 (19.12%) aligned >1 times 81.64% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4653095 / 29378923 = 0.1584 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 15:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:40:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:40:36: 1000000 INFO @ Tue, 02 Aug 2022 15:40:42: 2000000 INFO @ Tue, 02 Aug 2022 15:40:49: 3000000 INFO @ Tue, 02 Aug 2022 15:40:56: 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 15:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:40:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:03: 5000000 INFO @ Tue, 02 Aug 2022 15:41:05: 1000000 INFO @ Tue, 02 Aug 2022 15:41:10: 6000000 INFO @ Tue, 02 Aug 2022 15:41:12: 2000000 INFO @ Tue, 02 Aug 2022 15:41:17: 7000000 INFO @ Tue, 02 Aug 2022 15:41:19: 3000000 INFO @ Tue, 02 Aug 2022 15:41:24: 8000000 INFO @ Tue, 02 Aug 2022 15:41:26: 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 15:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 15:41:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:31: 9000000 INFO @ Tue, 02 Aug 2022 15:41:32: 5000000 INFO @ Tue, 02 Aug 2022 15:41:35: 1000000 INFO @ Tue, 02 Aug 2022 15:41:38: 10000000 INFO @ Tue, 02 Aug 2022 15:41:40: 6000000 INFO @ Tue, 02 Aug 2022 15:41:42: 2000000 INFO @ Tue, 02 Aug 2022 15:41:44: 11000000 INFO @ Tue, 02 Aug 2022 15:41:46: 7000000 INFO @ Tue, 02 Aug 2022 15:41:49: 3000000 INFO @ Tue, 02 Aug 2022 15:41:51: 12000000 INFO @ Tue, 02 Aug 2022 15:41:53: 8000000 INFO @ Tue, 02 Aug 2022 15:41:56: 4000000 INFO @ Tue, 02 Aug 2022 15:41:58: 13000000 INFO @ Tue, 02 Aug 2022 15:42:00: 9000000 INFO @ Tue, 02 Aug 2022 15:42:02: 5000000 INFO @ Tue, 02 Aug 2022 15:42:04: 14000000 INFO @ Tue, 02 Aug 2022 15:42:06: 10000000 INFO @ Tue, 02 Aug 2022 15:42:09: 6000000 INFO @ Tue, 02 Aug 2022 15:42:10: 15000000 INFO @ Tue, 02 Aug 2022 15:42:13: 11000000 INFO @ Tue, 02 Aug 2022 15:42:15: 7000000 INFO @ Tue, 02 Aug 2022 15:42:17: 16000000 INFO @ Tue, 02 Aug 2022 15:42:19: 12000000 INFO @ Tue, 02 Aug 2022 15:42:22: 8000000 INFO @ Tue, 02 Aug 2022 15:42:23: 17000000 INFO @ Tue, 02 Aug 2022 15:42:26: 13000000 INFO @ Tue, 02 Aug 2022 15:42:28: 9000000 INFO @ Tue, 02 Aug 2022 15:42:29: 18000000 INFO @ Tue, 02 Aug 2022 15:42:33: 14000000 INFO @ Tue, 02 Aug 2022 15:42:34: 10000000 INFO @ Tue, 02 Aug 2022 15:42:35: 19000000 INFO @ Tue, 02 Aug 2022 15:42:39: 15000000 INFO @ Tue, 02 Aug 2022 15:42:41: 11000000 INFO @ Tue, 02 Aug 2022 15:42:41: 20000000 INFO @ Tue, 02 Aug 2022 15:42:46: 16000000 INFO @ Tue, 02 Aug 2022 15:42:47: 12000000 INFO @ Tue, 02 Aug 2022 15:42:48: 21000000 INFO @ Tue, 02 Aug 2022 15:42:52: 17000000 INFO @ Tue, 02 Aug 2022 15:42:53: 13000000 INFO @ Tue, 02 Aug 2022 15:42:54: 22000000 INFO @ Tue, 02 Aug 2022 15:42:59: 18000000 INFO @ Tue, 02 Aug 2022 15:43:00: 23000000 INFO @ Tue, 02 Aug 2022 15:43:00: 14000000 INFO @ Tue, 02 Aug 2022 15:43:05: 19000000 INFO @ Tue, 02 Aug 2022 15:43:06: 24000000 INFO @ Tue, 02 Aug 2022 15:43:06: 15000000 INFO @ Tue, 02 Aug 2022 15:43:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:43:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:43:11: #1 total tags in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:43:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:11: #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 15:43:11: #1 tags after filtering in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:43:11: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:43:12: 20000000 INFO @ Tue, 02 Aug 2022 15:43:12: 16000000 INFO @ Tue, 02 Aug 2022 15:43:13: #2 number of paired peaks: 285 WARNING @ Tue, 02 Aug 2022 15:43:13: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 02 Aug 2022 15:43:13: start model_add_line... INFO @ Tue, 02 Aug 2022 15:43:13: start X-correlation... INFO @ Tue, 02 Aug 2022 15:43:13: end of X-cor INFO @ Tue, 02 Aug 2022 15:43:13: #2 finished! INFO @ Tue, 02 Aug 2022 15:43:13: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:43:13: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 02 Aug 2022 15:43:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05_model.r WARNING @ Tue, 02 Aug 2022 15:43:13: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:43:13: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 02 Aug 2022 15:43:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:43:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:18: 17000000 INFO @ Tue, 02 Aug 2022 15:43:18: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:43:24: 18000000 INFO @ Tue, 02 Aug 2022 15:43:25: 22000000 INFO @ Tue, 02 Aug 2022 15:43:29: 19000000 INFO @ Tue, 02 Aug 2022 15:43:31: 23000000 INFO @ Tue, 02 Aug 2022 15:43:35: 20000000 INFO @ Tue, 02 Aug 2022 15:43:37: 24000000 INFO @ Tue, 02 Aug 2022 15:43:41: 21000000 INFO @ Tue, 02 Aug 2022 15:43:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:43:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:43:42: #1 total tags in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:43:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:42: #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 15:43:43: #1 tags after filtering in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:43:43: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:43:45: #2 number of paired peaks: 285 WARNING @ Tue, 02 Aug 2022 15:43:45: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 02 Aug 2022 15:43:45: start model_add_line... INFO @ Tue, 02 Aug 2022 15:43:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:43:45: end of X-cor INFO @ Tue, 02 Aug 2022 15:43:45: #2 finished! INFO @ Tue, 02 Aug 2022 15:43:45: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:43:45: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 02 Aug 2022 15:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10_model.r WARNING @ Tue, 02 Aug 2022 15:43:45: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:43:45: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 02 Aug 2022 15:43:45: #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 15:43:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:43:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:47: 22000000 INFO @ Tue, 02 Aug 2022 15:43:53: 23000000 INFO @ Tue, 02 Aug 2022 15:43:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:43:59: 24000000 INFO @ Tue, 02 Aug 2022 15:44:03: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:44:03: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:44:03: #1 total tags in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:44:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:03: #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 15:44:04: #1 tags after filtering in treatment: 24725828 INFO @ Tue, 02 Aug 2022 15:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:44:04: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:05: #2 number of paired peaks: 285 WARNING @ Tue, 02 Aug 2022 15:44:05: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Tue, 02 Aug 2022 15:44:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:06: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:06: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:06: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:06: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:44:06: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 02 Aug 2022 15:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20_model.r WARNING @ Tue, 02 Aug 2022 15:44:06: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:44:06: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 02 Aug 2022 15:44:06: #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 15:44:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.05_summits.bed INFO @ Tue, 02 Aug 2022 15:44:15: Done! pass1 - making usageList (670 chroms): 2 millis pass2 - checking and writing primary data (5655 records, 4 fields): 46 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:44:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.10_summits.bed INFO @ Tue, 02 Aug 2022 15:44:49: Done! pass1 - making usageList (572 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227899/SRX13227899.20_summits.bed INFO @ Tue, 02 Aug 2022 15:45:07: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 40 millis CompletedMACS2peakCalling