Job ID = 6455276 SRX = SRX287656 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:40 prefetch.2.10.7: 1) Downloading 'SRR869843'... 2020-06-21T09:51:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:17 prefetch.2.10.7: 1) 'SRR869843' was downloaded successfully Read 16781682 spots for SRR869843/SRR869843.sra Written 16781682 spots for SRR869843/SRR869843.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: 00:05:43 16781682 reads; of these: 16781682 (100.00%) were unpaired; of these: 1275819 (7.60%) aligned 0 times 7981170 (47.56%) aligned exactly 1 time 7524693 (44.84%) aligned >1 times 92.40% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 3340538 / 15505863 = 0.2154 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 19:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.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 19:04:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:58: 1000000 INFO @ Sun, 21 Jun 2020 19:05:03: 2000000 INFO @ Sun, 21 Jun 2020 19:05:09: 3000000 INFO @ Sun, 21 Jun 2020 19:05:15: 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 19:05:20: 5000000 INFO @ Sun, 21 Jun 2020 19:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.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 19:05:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:26: 6000000 INFO @ Sun, 21 Jun 2020 19:05:27: 1000000 INFO @ Sun, 21 Jun 2020 19:05:32: 7000000 INFO @ Sun, 21 Jun 2020 19:05:34: 2000000 INFO @ Sun, 21 Jun 2020 19:05:38: 8000000 INFO @ Sun, 21 Jun 2020 19:05:40: 3000000 INFO @ Sun, 21 Jun 2020 19:05:45: 9000000 INFO @ Sun, 21 Jun 2020 19:05:46: 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 @ Sun, 21 Jun 2020 19:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.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 19:05:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:51: 10000000 INFO @ Sun, 21 Jun 2020 19:05:52: 5000000 INFO @ Sun, 21 Jun 2020 19:05:57: 1000000 INFO @ Sun, 21 Jun 2020 19:05:57: 11000000 INFO @ Sun, 21 Jun 2020 19:05:59: 6000000 INFO @ Sun, 21 Jun 2020 19:06:04: 2000000 INFO @ Sun, 21 Jun 2020 19:06:04: 12000000 INFO @ Sun, 21 Jun 2020 19:06:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:05: #1 total tags in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:06:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:05: #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 19:06:05: 7000000 INFO @ Sun, 21 Jun 2020 19:06:05: #1 tags after filtering in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:06: #2 number of paired peaks: 1087 INFO @ Sun, 21 Jun 2020 19:06:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:06: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:06:06: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 19:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05_model.r WARNING @ Sun, 21 Jun 2020 19:06:06: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:06:06: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 19:06:06: #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 19:06:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:10: 3000000 INFO @ Sun, 21 Jun 2020 19:06:12: 8000000 INFO @ Sun, 21 Jun 2020 19:06:16: 4000000 INFO @ Sun, 21 Jun 2020 19:06:18: 9000000 INFO @ Sun, 21 Jun 2020 19:06:23: 5000000 INFO @ Sun, 21 Jun 2020 19:06:25: 10000000 INFO @ Sun, 21 Jun 2020 19:06:29: 6000000 INFO @ Sun, 21 Jun 2020 19:06:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:31: 11000000 INFO @ Sun, 21 Jun 2020 19:06:35: 7000000 INFO @ Sun, 21 Jun 2020 19:06:38: 12000000 INFO @ Sun, 21 Jun 2020 19:06:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:39: #1 total tags in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:06:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:39: #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 19:06:39: #1 tags after filtering in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:06:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:40: #2 number of paired peaks: 1087 INFO @ Sun, 21 Jun 2020 19:06:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:40: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:06:40: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 19:06:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10_model.r WARNING @ Sun, 21 Jun 2020 19:06:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:06:40: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 19:06:40: #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 19:06:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:42: 8000000 INFO @ Sun, 21 Jun 2020 19:06:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:42: Done! pass1 - making usageList (914 chroms): 1 millis pass2 - checking and writing primary data (3864 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:06:47: 9000000 INFO @ Sun, 21 Jun 2020 19:06:54: 10000000 INFO @ Sun, 21 Jun 2020 19:07:00: 11000000 INFO @ Sun, 21 Jun 2020 19:07:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:06: 12000000 INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:07: #1 total tags in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:07:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:07: #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 19:07:07: #1 tags after filtering in treatment: 12165325 INFO @ Sun, 21 Jun 2020 19:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:08: #2 number of paired peaks: 1087 INFO @ Sun, 21 Jun 2020 19:07:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:08: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:07:08: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 19:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20_model.r WARNING @ Sun, 21 Jun 2020 19:07:08: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:07:08: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 19:07:08: #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 19:07:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:16: Done! pass1 - making usageList (710 chroms): 1 millis pass2 - checking and writing primary data (2357 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287656/SRX287656.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:43: Done! pass1 - making usageList (370 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 11 millis CompletedMACS2peakCalling