Job ID = 5720735 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,127,246 reads read : 24,254,492 reads written : 12,127,246 reads 0-length : 12,127,246 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: 00:05:24 12127246 reads; of these: 12127246 (100.00%) were unpaired; of these: 1076592 (8.88%) aligned 0 times 7682185 (63.35%) aligned exactly 1 time 3368469 (27.78%) aligned >1 times 91.12% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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 8 files... [bam_rmdupse_core] 1199475 / 11050654 = 0.1085 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 01:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.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 01:19:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:46: 1000000 INFO @ Thu, 16 Apr 2020 01:19:52: 2000000 INFO @ Thu, 16 Apr 2020 01:19:58: 3000000 INFO @ Thu, 16 Apr 2020 01:20:04: 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 01:20:10: 5000000 INFO @ Thu, 16 Apr 2020 01:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.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 01:20:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:17: 6000000 INFO @ Thu, 16 Apr 2020 01:20:19: 1000000 INFO @ Thu, 16 Apr 2020 01:20:24: 7000000 INFO @ Thu, 16 Apr 2020 01:20:26: 2000000 INFO @ Thu, 16 Apr 2020 01:20:31: 8000000 INFO @ Thu, 16 Apr 2020 01:20:33: 3000000 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 01:20:38: 9000000 INFO @ Thu, 16 Apr 2020 01:20:40: 4000000 INFO @ Thu, 16 Apr 2020 01:20:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.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 01:20:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:20:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:20:45: #1 total tags in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:20:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:45: #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 01:20:45: #1 tags after filtering in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:20:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:45: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:46: #2 number of paired peaks: 890 WARNING @ Thu, 16 Apr 2020 01:20:46: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Thu, 16 Apr 2020 01:20:46: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:46: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:46: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:46: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:46: #2 predicted fragment length is 91 bps INFO @ Thu, 16 Apr 2020 01:20:46: #2 alternative fragment length(s) may be 91 bps INFO @ Thu, 16 Apr 2020 01:20:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:46: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:46: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Thu, 16 Apr 2020 01:20:46: #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 01:20:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:47: 5000000 INFO @ Thu, 16 Apr 2020 01:20:49: 1000000 INFO @ Thu, 16 Apr 2020 01:20:55: 6000000 INFO @ Thu, 16 Apr 2020 01:20:56: 2000000 INFO @ Thu, 16 Apr 2020 01:21:02: 7000000 INFO @ Thu, 16 Apr 2020 01:21:04: 3000000 INFO @ Thu, 16 Apr 2020 01:21:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:10: 8000000 INFO @ Thu, 16 Apr 2020 01:21:11: 4000000 INFO @ Thu, 16 Apr 2020 01:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.05_summits.bed INFO @ Thu, 16 Apr 2020 01:21:16: Done! INFO @ Thu, 16 Apr 2020 01:21:17: 9000000 INFO @ Thu, 16 Apr 2020 01:21:18: 5000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3570 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:23: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:23: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:23: #1 total tags in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:21:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:23: #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 01:21:23: #1 tags after filtering in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:23: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:24: #2 number of paired peaks: 890 WARNING @ Thu, 16 Apr 2020 01:21:24: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:24: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:24: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:24: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:24: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:24: #2 predicted fragment length is 91 bps INFO @ Thu, 16 Apr 2020 01:21:24: #2 alternative fragment length(s) may be 91 bps INFO @ Thu, 16 Apr 2020 01:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:24: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:24: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Thu, 16 Apr 2020 01:21:24: #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 01:21:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:25: 6000000 INFO @ Thu, 16 Apr 2020 01:21:32: 7000000 INFO @ Thu, 16 Apr 2020 01:21:39: 8000000 INFO @ Thu, 16 Apr 2020 01:21:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:45: 9000000 INFO @ Thu, 16 Apr 2020 01:21:51: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:51: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:51: #1 total tags in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:21:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:51: #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 01:21:51: #1 tags after filtering in treatment: 9851179 INFO @ Thu, 16 Apr 2020 01:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:51: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:52: #2 number of paired peaks: 890 WARNING @ Thu, 16 Apr 2020 01:21:52: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:52: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:52: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:52: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:52: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:52: #2 predicted fragment length is 91 bps INFO @ Thu, 16 Apr 2020 01:21:52: #2 alternative fragment length(s) may be 91 bps INFO @ Thu, 16 Apr 2020 01:21:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20_model.r WARNING @ Thu, 16 Apr 2020 01:21:52: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:52: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Thu, 16 Apr 2020 01:21:52: #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 01:21:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.10_summits.bed INFO @ Thu, 16 Apr 2020 01:21:56: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2040 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:22:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226974/SRX5226974.20_summits.bed INFO @ Thu, 16 Apr 2020 01:22:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (867 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。