Job ID = 6509086 SRX = SRX645129 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:28:22 prefetch.2.10.7: 1) Downloading 'SRR1505729'... 2020-06-26T15:28:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:32:48 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:32:48 prefetch.2.10.7: 1) 'SRR1505729' was downloaded successfully Read 32790775 spots for SRR1505729/SRR1505729.sra Written 32790775 spots for SRR1505729/SRR1505729.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:36 32790775 reads; of these: 32790775 (100.00%) were unpaired; of these: 18552962 (56.58%) aligned 0 times 10939125 (33.36%) aligned exactly 1 time 3298688 (10.06%) aligned >1 times 43.42% overall alignment rate Time searching: 00:12:37 Overall time: 00:12:37 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] 11026309 / 14237813 = 0.7744 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 @ Sat, 27 Jun 2020 00:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.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 @ Sat, 27 Jun 2020 00:51:59: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:51:59: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:52:07: 1000000 INFO @ Sat, 27 Jun 2020 00:52:15: 2000000 INFO @ Sat, 27 Jun 2020 00:52:23: 3000000 INFO @ Sat, 27 Jun 2020 00:52:25: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:52:25: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:52:25: #1 total tags in treatment: 3211504 INFO @ Sat, 27 Jun 2020 00:52:25: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:52:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:52:25: #1 tags after filtering in treatment: 3211438 INFO @ Sat, 27 Jun 2020 00:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:52:25: #1 finished! INFO @ Sat, 27 Jun 2020 00:52:25: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:52:26: #2 number of paired peaks: 3355 INFO @ Sat, 27 Jun 2020 00:52:26: start model_add_line... INFO @ Sat, 27 Jun 2020 00:52:26: start X-correlation... INFO @ Sat, 27 Jun 2020 00:52:26: end of X-cor INFO @ Sat, 27 Jun 2020 00:52:26: #2 finished! INFO @ Sat, 27 Jun 2020 00:52:26: #2 predicted fragment length is 106 bps INFO @ Sat, 27 Jun 2020 00:52:26: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 27 Jun 2020 00:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05_model.r WARNING @ Sat, 27 Jun 2020 00:52:26: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:52:26: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 27 Jun 2020 00:52:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:52:26: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:52:26: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 27 Jun 2020 00:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.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 @ Sat, 27 Jun 2020 00:52:29: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:52:29: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:52:36: 1000000 INFO @ Sat, 27 Jun 2020 00:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.05_summits.bed INFO @ Sat, 27 Jun 2020 00:52:38: Done! pass1 - making usageList (692 chroms): 2 millis pass2 - checking and writing primary data (2402 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:52:44: 2000000 INFO @ Sat, 27 Jun 2020 00:52:52: 3000000 INFO @ Sat, 27 Jun 2020 00:52:54: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:52:54: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:52:54: #1 total tags in treatment: 3211504 INFO @ Sat, 27 Jun 2020 00:52:54: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:52:54: #1 tags after filtering in treatment: 3211438 INFO @ Sat, 27 Jun 2020 00:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:52:54: #1 finished! INFO @ Sat, 27 Jun 2020 00:52:54: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:52:55: #2 number of paired peaks: 3355 INFO @ Sat, 27 Jun 2020 00:52:55: start model_add_line... INFO @ Sat, 27 Jun 2020 00:52:55: start X-correlation... INFO @ Sat, 27 Jun 2020 00:52:55: end of X-cor INFO @ Sat, 27 Jun 2020 00:52:55: #2 finished! INFO @ Sat, 27 Jun 2020 00:52:55: #2 predicted fragment length is 106 bps INFO @ Sat, 27 Jun 2020 00:52:55: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 27 Jun 2020 00:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10_model.r WARNING @ Sat, 27 Jun 2020 00:52:55: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:52:55: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 27 Jun 2020 00:52:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:52:55: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:52:55: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 27 Jun 2020 00:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.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 @ Sat, 27 Jun 2020 00:52:59: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:52:59: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:53:07: 1000000 INFO @ Sat, 27 Jun 2020 00:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.10_summits.bed INFO @ Sat, 27 Jun 2020 00:53:08: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (1386 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:53:15: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:53:23: 3000000 INFO @ Sat, 27 Jun 2020 00:53:25: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:53:25: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:53:25: #1 total tags in treatment: 3211504 INFO @ Sat, 27 Jun 2020 00:53:25: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:53:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:53:25: #1 tags after filtering in treatment: 3211438 INFO @ Sat, 27 Jun 2020 00:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:53:25: #1 finished! INFO @ Sat, 27 Jun 2020 00:53:25: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:53:26: #2 number of paired peaks: 3355 INFO @ Sat, 27 Jun 2020 00:53:26: start model_add_line... INFO @ Sat, 27 Jun 2020 00:53:26: start X-correlation... INFO @ Sat, 27 Jun 2020 00:53:26: end of X-cor INFO @ Sat, 27 Jun 2020 00:53:26: #2 finished! INFO @ Sat, 27 Jun 2020 00:53:26: #2 predicted fragment length is 106 bps INFO @ Sat, 27 Jun 2020 00:53:26: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 27 Jun 2020 00:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20_model.r WARNING @ Sat, 27 Jun 2020 00:53:26: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:53:26: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 27 Jun 2020 00:53:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:53:26: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:53:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:53:34: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645129/SRX645129.20_summits.bed INFO @ Sat, 27 Jun 2020 00:53:38: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 13 millis CompletedMACS2peakCalling