Job ID = 6455509 SRX = SRX287843 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:10 prefetch.2.10.7: 1) Downloading 'SRR870032'... 2020-06-21T09:57:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:10 prefetch.2.10.7: 'SRR870032' is valid 2020-06-21T09:59:10 prefetch.2.10.7: 1) 'SRR870032' was downloaded successfully Read 13478686 spots for SRR870032/SRR870032.sra Written 13478686 spots for SRR870032/SRR870032.sra 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: 00:00:01 Multiseed full-index search: 00:04:08 13478686 reads; of these: 13478686 (100.00%) were unpaired; of these: 741441 (5.50%) aligned 0 times 9407409 (69.79%) aligned exactly 1 time 3329836 (24.70%) aligned >1 times 94.50% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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 8 files... [bam_rmdupse_core] 2215823 / 12737245 = 0.1740 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 @ Sun, 21 Jun 2020 19:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.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 @ Sun, 21 Jun 2020 19:07:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:54: 1000000 INFO @ Sun, 21 Jun 2020 19:08:00: 2000000 INFO @ Sun, 21 Jun 2020 19:08:05: 3000000 INFO @ Sun, 21 Jun 2020 19:08:11: 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 @ Sun, 21 Jun 2020 19:08:17: 5000000 INFO @ Sun, 21 Jun 2020 19:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.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 @ Sun, 21 Jun 2020 19:08:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:24: 6000000 INFO @ Sun, 21 Jun 2020 19:08:26: 1000000 INFO @ Sun, 21 Jun 2020 19:08:30: 7000000 INFO @ Sun, 21 Jun 2020 19:08:33: 2000000 INFO @ Sun, 21 Jun 2020 19:08:37: 8000000 INFO @ Sun, 21 Jun 2020 19:08:40: 3000000 INFO @ Sun, 21 Jun 2020 19:08:44: 9000000 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 @ Sun, 21 Jun 2020 19:08:47: 4000000 INFO @ Sun, 21 Jun 2020 19:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.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 @ Sun, 21 Jun 2020 19:08:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:51: 10000000 INFO @ Sun, 21 Jun 2020 19:08:54: 5000000 INFO @ Sun, 21 Jun 2020 19:08:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:55: #1 total tags in treatment: 10521422 INFO @ Sun, 21 Jun 2020 19:08:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:08:55: 1000000 INFO @ Sun, 21 Jun 2020 19:08:55: #1 tags after filtering in treatment: 10521418 INFO @ Sun, 21 Jun 2020 19:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:56: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 19:08:56: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 19:08:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:56: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 19:08:56: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 19:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05_model.r WARNING @ Sun, 21 Jun 2020 19:08:56: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:08:56: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 19:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:08:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:00: 6000000 INFO @ Sun, 21 Jun 2020 19:09:02: 2000000 INFO @ Sun, 21 Jun 2020 19:09:07: 7000000 INFO @ Sun, 21 Jun 2020 19:09:09: 3000000 INFO @ Sun, 21 Jun 2020 19:09:14: 8000000 INFO @ Sun, 21 Jun 2020 19:09:16: 4000000 INFO @ Sun, 21 Jun 2020 19:09:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:21: 9000000 INFO @ Sun, 21 Jun 2020 19:09:23: 5000000 INFO @ Sun, 21 Jun 2020 19:09:28: 10000000 INFO @ Sun, 21 Jun 2020 19:09:30: 6000000 INFO @ Sun, 21 Jun 2020 19:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:31: Done! pass1 - making usageList (648 chroms): 2 millis pass2 - checking and writing primary data (2916 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:32: #1 total tags in treatment: 10521422 INFO @ Sun, 21 Jun 2020 19:09:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:32: #1 tags after filtering in treatment: 10521418 INFO @ Sun, 21 Jun 2020 19:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:33: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 19:09:33: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:33: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 19:09:33: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 19:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:33: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:33: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 19:09:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:09:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:36: 7000000 INFO @ Sun, 21 Jun 2020 19:09:42: 8000000 INFO @ Sun, 21 Jun 2020 19:09:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:55: 10000000 INFO @ Sun, 21 Jun 2020 19:09:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:58: #1 total tags in treatment: 10521422 INFO @ Sun, 21 Jun 2020 19:09:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:09:59: #1 tags after filtering in treatment: 10521418 INFO @ Sun, 21 Jun 2020 19:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:00: #2 number of paired peaks: 446 WARNING @ Sun, 21 Jun 2020 19:10:00: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:00: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 19:10:00: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 19:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:00: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:00: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 19:10:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:10:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:08: Done! pass1 - making usageList (484 chroms): 1 millis pass2 - checking and writing primary data (1318 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287843/SRX287843.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:33: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 6 millis CompletedMACS2peakCalling