Job ID = 5720742 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,635,978 reads read : 47,271,956 reads written : 23,635,978 reads 0-length : 23,635,978 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:11:06 23635978 reads; of these: 23635978 (100.00%) were unpaired; of these: 1007939 (4.26%) aligned 0 times 16753846 (70.88%) aligned exactly 1 time 5874193 (24.85%) aligned >1 times 95.74% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2784999 / 22628039 = 0.1231 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 @ Thu, 16 Apr 2020 01:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.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 @ Thu, 16 Apr 2020 01:35:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:35:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:35:11: 1000000 INFO @ Thu, 16 Apr 2020 01:35:17: 2000000 INFO @ Thu, 16 Apr 2020 01:35:23: 3000000 INFO @ Thu, 16 Apr 2020 01:35:29: 4000000 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 @ Thu, 16 Apr 2020 01:35:35: 5000000 INFO @ Thu, 16 Apr 2020 01:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.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 @ Thu, 16 Apr 2020 01:35:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:35:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:35:41: 6000000 INFO @ Thu, 16 Apr 2020 01:35:42: 1000000 INFO @ Thu, 16 Apr 2020 01:35:47: 7000000 INFO @ Thu, 16 Apr 2020 01:35:48: 2000000 INFO @ Thu, 16 Apr 2020 01:35:53: 8000000 INFO @ Thu, 16 Apr 2020 01:35:53: 3000000 INFO @ Thu, 16 Apr 2020 01:35:59: 9000000 INFO @ Thu, 16 Apr 2020 01:36:00: 4000000 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 @ Thu, 16 Apr 2020 01:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.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 @ Thu, 16 Apr 2020 01:36:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:36:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:36:06: 10000000 INFO @ Thu, 16 Apr 2020 01:36:06: 5000000 INFO @ Thu, 16 Apr 2020 01:36:11: 1000000 INFO @ Thu, 16 Apr 2020 01:36:13: 11000000 INFO @ Thu, 16 Apr 2020 01:36:13: 6000000 INFO @ Thu, 16 Apr 2020 01:36:17: 2000000 INFO @ Thu, 16 Apr 2020 01:36:19: 12000000 INFO @ Thu, 16 Apr 2020 01:36:20: 7000000 INFO @ Thu, 16 Apr 2020 01:36:23: 3000000 INFO @ Thu, 16 Apr 2020 01:36:26: 13000000 INFO @ Thu, 16 Apr 2020 01:36:26: 8000000 INFO @ Thu, 16 Apr 2020 01:36:28: 4000000 INFO @ Thu, 16 Apr 2020 01:36:32: 14000000 INFO @ Thu, 16 Apr 2020 01:36:32: 9000000 INFO @ Thu, 16 Apr 2020 01:36:34: 5000000 INFO @ Thu, 16 Apr 2020 01:36:38: 15000000 INFO @ Thu, 16 Apr 2020 01:36:39: 10000000 INFO @ Thu, 16 Apr 2020 01:36:39: 6000000 INFO @ Thu, 16 Apr 2020 01:36:45: 16000000 INFO @ Thu, 16 Apr 2020 01:36:45: 7000000 INFO @ Thu, 16 Apr 2020 01:36:45: 11000000 INFO @ Thu, 16 Apr 2020 01:36:50: 8000000 INFO @ Thu, 16 Apr 2020 01:36:51: 17000000 INFO @ Thu, 16 Apr 2020 01:36:51: 12000000 INFO @ Thu, 16 Apr 2020 01:36:56: 9000000 INFO @ Thu, 16 Apr 2020 01:36:57: 18000000 INFO @ Thu, 16 Apr 2020 01:36:58: 13000000 INFO @ Thu, 16 Apr 2020 01:37:01: 10000000 INFO @ Thu, 16 Apr 2020 01:37:04: 19000000 INFO @ Thu, 16 Apr 2020 01:37:04: 14000000 INFO @ Thu, 16 Apr 2020 01:37:07: 11000000 INFO @ Thu, 16 Apr 2020 01:37:09: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:37:09: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:37:09: #1 total tags in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:37:09: #1 tags after filtering in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:37:09: #1 finished! INFO @ Thu, 16 Apr 2020 01:37:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:37:10: 15000000 INFO @ Thu, 16 Apr 2020 01:37:11: #2 number of paired peaks: 525 WARNING @ Thu, 16 Apr 2020 01:37:11: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Thu, 16 Apr 2020 01:37:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:37:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:37:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:37:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:37:11: #2 predicted fragment length is 67 bps INFO @ Thu, 16 Apr 2020 01:37:11: #2 alternative fragment length(s) may be 4,67 bps INFO @ Thu, 16 Apr 2020 01:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05_model.r WARNING @ Thu, 16 Apr 2020 01:37:11: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:37:11: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Thu, 16 Apr 2020 01:37:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:37:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:37:12: 12000000 INFO @ Thu, 16 Apr 2020 01:37:17: 16000000 INFO @ Thu, 16 Apr 2020 01:37:18: 13000000 INFO @ Thu, 16 Apr 2020 01:37:23: 17000000 INFO @ Thu, 16 Apr 2020 01:37:23: 14000000 INFO @ Thu, 16 Apr 2020 01:37:29: 15000000 INFO @ Thu, 16 Apr 2020 01:37:29: 18000000 INFO @ Thu, 16 Apr 2020 01:37:34: 16000000 INFO @ Thu, 16 Apr 2020 01:37:35: 19000000 INFO @ Thu, 16 Apr 2020 01:37:40: 17000000 INFO @ Thu, 16 Apr 2020 01:37:40: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:37:40: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:37:40: #1 total tags in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:37:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:37:41: #1 tags after filtering in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:37:41: #1 finished! INFO @ Thu, 16 Apr 2020 01:37:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:37:42: #2 number of paired peaks: 525 WARNING @ Thu, 16 Apr 2020 01:37:42: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Thu, 16 Apr 2020 01:37:42: start model_add_line... INFO @ Thu, 16 Apr 2020 01:37:42: start X-correlation... INFO @ Thu, 16 Apr 2020 01:37:42: end of X-cor INFO @ Thu, 16 Apr 2020 01:37:42: #2 finished! INFO @ Thu, 16 Apr 2020 01:37:42: #2 predicted fragment length is 67 bps INFO @ Thu, 16 Apr 2020 01:37:42: #2 alternative fragment length(s) may be 4,67 bps INFO @ Thu, 16 Apr 2020 01:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10_model.r WARNING @ Thu, 16 Apr 2020 01:37:42: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:37:42: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Thu, 16 Apr 2020 01:37:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:37:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:37:45: 18000000 INFO @ Thu, 16 Apr 2020 01:37:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:37:51: 19000000 INFO @ Thu, 16 Apr 2020 01:37:55: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:37:55: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:37:55: #1 total tags in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:37:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:37:56: #1 tags after filtering in treatment: 19843040 INFO @ Thu, 16 Apr 2020 01:37:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:37:56: #1 finished! INFO @ Thu, 16 Apr 2020 01:37:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:37:57: #2 number of paired peaks: 525 WARNING @ Thu, 16 Apr 2020 01:37:57: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Thu, 16 Apr 2020 01:37:57: start model_add_line... INFO @ Thu, 16 Apr 2020 01:37:57: start X-correlation... INFO @ Thu, 16 Apr 2020 01:37:57: end of X-cor INFO @ Thu, 16 Apr 2020 01:37:57: #2 finished! INFO @ Thu, 16 Apr 2020 01:37:57: #2 predicted fragment length is 67 bps INFO @ Thu, 16 Apr 2020 01:37:57: #2 alternative fragment length(s) may be 4,67 bps INFO @ Thu, 16 Apr 2020 01:37:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20_model.r WARNING @ Thu, 16 Apr 2020 01:37:57: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:37:57: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Thu, 16 Apr 2020 01:37:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:37:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:38:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:38:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:38:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.05_summits.bed INFO @ Thu, 16 Apr 2020 01:38:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5900 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:38:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:38:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:38:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:38:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.10_summits.bed INFO @ Thu, 16 Apr 2020 01:38:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2845 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226981/SRX5226981.20_summits.bed INFO @ Thu, 16 Apr 2020 01:38:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1069 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。