Job ID = 6455438 SRX = SRX287789 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:59:10 prefetch.2.10.7: 1) Downloading 'SRR869978'... 2020-06-21T09:59:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:03 prefetch.2.10.7: 'SRR869978' is valid 2020-06-21T10:01:03 prefetch.2.10.7: 1) 'SRR869978' was downloaded successfully Read 14916545 spots for SRR869978/SRR869978.sra Written 14916545 spots for SRR869978/SRR869978.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: 00:00:00 Multiseed full-index search: 00:04:58 14916545 reads; of these: 14916545 (100.00%) were unpaired; of these: 1177138 (7.89%) aligned 0 times 8826116 (59.17%) aligned exactly 1 time 4913291 (32.94%) aligned >1 times 92.11% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 4521035 / 13739407 = 0.3291 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 19:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.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 19:11:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:31: 1000000 INFO @ Sun, 21 Jun 2020 19:11:36: 2000000 INFO @ Sun, 21 Jun 2020 19:11:41: 3000000 INFO @ Sun, 21 Jun 2020 19:11:46: 4000000 INFO @ Sun, 21 Jun 2020 19:11:50: 5000000 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 19:11:55: 6000000 INFO @ Sun, 21 Jun 2020 19:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.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 19:11:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:00: 7000000 INFO @ Sun, 21 Jun 2020 19:12:01: 1000000 INFO @ Sun, 21 Jun 2020 19:12:06: 2000000 INFO @ Sun, 21 Jun 2020 19:12:07: 8000000 INFO @ Sun, 21 Jun 2020 19:12:11: 3000000 INFO @ Sun, 21 Jun 2020 19:12:12: 9000000 INFO @ Sun, 21 Jun 2020 19:12:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:13: #1 total tags in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:12:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:13: #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 19:12:14: #1 tags after filtering in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:15: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 19:12:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:15: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:12:15: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:15: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:12:15: #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 19:12:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:16: 4000000 INFO @ Sun, 21 Jun 2020 19:12:21: 5000000 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 19:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.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 19:12:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:27: 6000000 INFO @ Sun, 21 Jun 2020 19:12:31: 1000000 INFO @ Sun, 21 Jun 2020 19:12:31: 7000000 INFO @ Sun, 21 Jun 2020 19:12:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:36: 2000000 INFO @ Sun, 21 Jun 2020 19:12:37: 8000000 INFO @ Sun, 21 Jun 2020 19:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.05_summits.bed INFO @ Sun, 21 Jun 2020 19:12:40: Done! pass1 - making usageList (609 chroms): 2 millis pass2 - checking and writing primary data (2218 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:41: 3000000 INFO @ Sun, 21 Jun 2020 19:12:43: 9000000 INFO @ Sun, 21 Jun 2020 19:12:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:44: #1 total tags in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:12:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:44: #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 19:12:45: #1 tags after filtering in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:45: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 19:12:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:45: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:12:45: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:45: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:45: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:12:45: #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 19:12:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:46: 4000000 INFO @ Sun, 21 Jun 2020 19:12:51: 5000000 INFO @ Sun, 21 Jun 2020 19:12:56: 6000000 INFO @ Sun, 21 Jun 2020 19:13:01: 7000000 INFO @ Sun, 21 Jun 2020 19:13:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:06: 8000000 INFO @ Sun, 21 Jun 2020 19:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:11: Done! pass1 - making usageList (500 chroms): 2 millis pass2 - checking and writing primary data (1896 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:11: 9000000 INFO @ Sun, 21 Jun 2020 19:13:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:13: #1 total tags in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:13:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:13: #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 19:13:14: #1 tags after filtering in treatment: 9218372 INFO @ Sun, 21 Jun 2020 19:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:14: #2 number of paired peaks: 1041 INFO @ Sun, 21 Jun 2020 19:13:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:15: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:13:15: #2 alternative fragment length(s) may be 4,41 bps INFO @ Sun, 21 Jun 2020 19:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:15: #2 You may need to consider one of the other alternative d(s): 4,41 WARNING @ Sun, 21 Jun 2020 19:13:15: #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 19:13:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287789/SRX287789.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:40: Done! pass1 - making usageList (374 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。