Job ID = 6452956 SRX = SRX066244 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:23 prefetch.2.10.7: 1) Downloading 'SRR222069'... 2020-06-21T07:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:26 prefetch.2.10.7: 'SRR222069' is valid 2020-06-21T08:01:26 prefetch.2.10.7: 1) 'SRR222069' was downloaded successfully Read 19544210 spots for SRR222069/SRR222069.sra Written 19544210 spots for SRR222069/SRR222069.sra 2020-06-21T08:02:28 prefetch.2.10.7: 1) Downloading 'SRR222070'... 2020-06-21T08:02:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:59 prefetch.2.10.7: 'SRR222070' is valid 2020-06-21T08:04:59 prefetch.2.10.7: 1) 'SRR222070' was downloaded successfully Read 6154521 spots for SRR222070/SRR222070.sra Written 6154521 spots for SRR222070/SRR222070.sra 2020-06-21T08:05:27 prefetch.2.10.7: 1) Downloading 'SRR222071'... 2020-06-21T08:05:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:15 prefetch.2.10.7: 'SRR222071' is valid 2020-06-21T08:07:15 prefetch.2.10.7: 1) 'SRR222071' was downloaded successfully Read 21380857 spots for SRR222071/SRR222071.sra Written 21380857 spots for SRR222071/SRR222071.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: 00:07:41 47079588 reads; of these: 47079588 (100.00%) were unpaired; of these: 19772338 (42.00%) aligned 0 times 20611022 (43.78%) aligned exactly 1 time 6696228 (14.22%) aligned >1 times 58.00% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 18106129 / 27307250 = 0.6631 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 17:20:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.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 17:20:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:53: 1000000 INFO @ Sun, 21 Jun 2020 17:20:58: 2000000 INFO @ Sun, 21 Jun 2020 17:21:03: 3000000 INFO @ Sun, 21 Jun 2020 17:21:08: 4000000 INFO @ Sun, 21 Jun 2020 17:21:13: 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 17:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.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 17:21:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:18: 6000000 INFO @ Sun, 21 Jun 2020 17:21:22: 1000000 INFO @ Sun, 21 Jun 2020 17:21:23: 7000000 INFO @ Sun, 21 Jun 2020 17:21:27: 2000000 INFO @ Sun, 21 Jun 2020 17:21:29: 8000000 INFO @ Sun, 21 Jun 2020 17:21:32: 3000000 INFO @ Sun, 21 Jun 2020 17:21:34: 9000000 INFO @ Sun, 21 Jun 2020 17:21:35: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:35: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:35: #1 total tags in treatment: 9201121 INFO @ Sun, 21 Jun 2020 17:21:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:35: #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 17:21:36: #1 tags after filtering in treatment: 9201118 INFO @ Sun, 21 Jun 2020 17:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:36: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 17:21:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:36: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 17:21:36: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 17:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05_model.r WARNING @ Sun, 21 Jun 2020 17:21:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:21:36: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 17:21:36: #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 17:21:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:37: 4000000 INFO @ Sun, 21 Jun 2020 17:21:42: 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 17:21:47: 6000000 INFO @ Sun, 21 Jun 2020 17:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.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 17:21:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:52: 1000000 INFO @ Sun, 21 Jun 2020 17:21:52: 7000000 INFO @ Sun, 21 Jun 2020 17:21:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:57: 2000000 INFO @ Sun, 21 Jun 2020 17:21:57: 8000000 INFO @ Sun, 21 Jun 2020 17:22:02: 3000000 INFO @ Sun, 21 Jun 2020 17:22:02: 9000000 INFO @ Sun, 21 Jun 2020 17:22:03: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:03: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:03: #1 total tags in treatment: 9201121 INFO @ Sun, 21 Jun 2020 17:22:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:03: #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 17:22:03: #1 tags after filtering in treatment: 9201118 INFO @ Sun, 21 Jun 2020 17:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:04: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 17:22:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:04: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 17:22:04: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 17:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10_model.r WARNING @ Sun, 21 Jun 2020 17:22:04: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:04: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 17:22:04: #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 17:22:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:06: 4000000 INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.05_summits.bed INFO @ Sun, 21 Jun 2020 17:22:07: Done! pass1 - making usageList (679 chroms): 2 millis pass2 - checking and writing primary data (4506 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:22:11: 5000000 INFO @ Sun, 21 Jun 2020 17:22:16: 6000000 INFO @ Sun, 21 Jun 2020 17:22:21: 7000000 INFO @ Sun, 21 Jun 2020 17:22:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:26: 8000000 INFO @ Sun, 21 Jun 2020 17:22:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:22:32: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:32: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:32: #1 total tags in treatment: 9201121 INFO @ Sun, 21 Jun 2020 17:22:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:32: #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 17:22:32: #1 tags after filtering in treatment: 9201118 INFO @ Sun, 21 Jun 2020 17:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:33: #2 number of paired peaks: 1340 INFO @ Sun, 21 Jun 2020 17:22:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:33: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 17:22:33: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 17:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20_model.r WARNING @ Sun, 21 Jun 2020 17:22:33: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:33: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 17:22:33: #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 17:22:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.10_summits.bed INFO @ Sun, 21 Jun 2020 17:22:33: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (2851 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:22:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066244/SRX066244.20_summits.bed INFO @ Sun, 21 Jun 2020 17:23:01: Done! pass1 - making usageList (358 chroms): 1 millis pass2 - checking and writing primary data (1048 records, 4 fields): 11 millis CompletedMACS2peakCalling