Job ID = 6453588 SRX = SRX128303 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:36:24 prefetch.2.10.7: 1) Downloading 'SRR442242'... 2020-06-21T08:36:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:24 prefetch.2.10.7: 1) 'SRR442242' was downloaded successfully Read 31546612 spots for SRR442242/SRR442242.sra Written 31546612 spots for SRR442242/SRR442242.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: 00:06:38 31546612 reads; of these: 31546612 (100.00%) were unpaired; of these: 1784972 (5.66%) aligned 0 times 21530873 (68.25%) aligned exactly 1 time 8230767 (26.09%) aligned >1 times 94.34% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 13643728 / 29761640 = 0.4584 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 17:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.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 17:56:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:57: 1000000 INFO @ Sun, 21 Jun 2020 17:57:02: 2000000 INFO @ Sun, 21 Jun 2020 17:57:07: 3000000 INFO @ Sun, 21 Jun 2020 17:57:12: 4000000 INFO @ Sun, 21 Jun 2020 17:57:17: 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 17:57:22: 6000000 INFO @ Sun, 21 Jun 2020 17:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.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 17:57:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:28: 7000000 INFO @ Sun, 21 Jun 2020 17:57:29: 1000000 INFO @ Sun, 21 Jun 2020 17:57:34: 8000000 INFO @ Sun, 21 Jun 2020 17:57:35: 2000000 INFO @ Sun, 21 Jun 2020 17:57:40: 9000000 INFO @ Sun, 21 Jun 2020 17:57:42: 3000000 INFO @ Sun, 21 Jun 2020 17:57:46: 10000000 INFO @ Sun, 21 Jun 2020 17:57:48: 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 17:57:52: 11000000 INFO @ Sun, 21 Jun 2020 17:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.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 17:57:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:55: 5000000 INFO @ Sun, 21 Jun 2020 17:57:58: 12000000 INFO @ Sun, 21 Jun 2020 17:57:59: 1000000 INFO @ Sun, 21 Jun 2020 17:58:01: 6000000 INFO @ Sun, 21 Jun 2020 17:58:04: 13000000 INFO @ Sun, 21 Jun 2020 17:58:06: 2000000 INFO @ Sun, 21 Jun 2020 17:58:08: 7000000 INFO @ Sun, 21 Jun 2020 17:58:11: 14000000 INFO @ Sun, 21 Jun 2020 17:58:12: 3000000 INFO @ Sun, 21 Jun 2020 17:58:14: 8000000 INFO @ Sun, 21 Jun 2020 17:58:17: 15000000 INFO @ Sun, 21 Jun 2020 17:58:19: 4000000 INFO @ Sun, 21 Jun 2020 17:58:21: 9000000 INFO @ Sun, 21 Jun 2020 17:58:23: 16000000 INFO @ Sun, 21 Jun 2020 17:58:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:58:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:58:24: #1 total tags in treatment: 16117912 INFO @ Sun, 21 Jun 2020 17:58:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:24: #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 17:58:24: #1 tags after filtering in treatment: 16117869 INFO @ Sun, 21 Jun 2020 17:58:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:25: 5000000 INFO @ Sun, 21 Jun 2020 17:58:26: #2 number of paired peaks: 4120 INFO @ Sun, 21 Jun 2020 17:58:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:26: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:58:26: #2 alternative fragment length(s) may be 4,81 bps INFO @ Sun, 21 Jun 2020 17:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05_model.r INFO @ Sun, 21 Jun 2020 17:58:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:27: 10000000 INFO @ Sun, 21 Jun 2020 17:58:32: 6000000 INFO @ Sun, 21 Jun 2020 17:58:34: 11000000 INFO @ Sun, 21 Jun 2020 17:58:38: 7000000 INFO @ Sun, 21 Jun 2020 17:58:40: 12000000 INFO @ Sun, 21 Jun 2020 17:58:45: 8000000 INFO @ Sun, 21 Jun 2020 17:58:47: 13000000 INFO @ Sun, 21 Jun 2020 17:58:51: 9000000 INFO @ Sun, 21 Jun 2020 17:58:53: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:58:58: 10000000 INFO @ Sun, 21 Jun 2020 17:58:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:59: 15000000 INFO @ Sun, 21 Jun 2020 17:59:04: 11000000 INFO @ Sun, 21 Jun 2020 17:59:06: 16000000 INFO @ Sun, 21 Jun 2020 17:59:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:59:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:59:07: #1 total tags in treatment: 16117912 INFO @ Sun, 21 Jun 2020 17:59:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:07: #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 17:59:07: #1 tags after filtering in treatment: 16117869 INFO @ Sun, 21 Jun 2020 17:59:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:09: #2 number of paired peaks: 4120 INFO @ Sun, 21 Jun 2020 17:59:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:09: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:59:09: #2 alternative fragment length(s) may be 4,81 bps INFO @ Sun, 21 Jun 2020 17:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10_model.r INFO @ Sun, 21 Jun 2020 17:59:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:11: 12000000 INFO @ Sun, 21 Jun 2020 17:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:17: Done! INFO @ Sun, 21 Jun 2020 17:59:17: 13000000 pass1 - making usageList (721 chroms): 3 millis pass2 - checking and writing primary data (14149 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:23: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:59:29: 15000000 INFO @ Sun, 21 Jun 2020 17:59:35: 16000000 INFO @ Sun, 21 Jun 2020 17:59:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:59:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:59:36: #1 total tags in treatment: 16117912 INFO @ Sun, 21 Jun 2020 17:59:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:36: #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 17:59:36: #1 tags after filtering in treatment: 16117869 INFO @ Sun, 21 Jun 2020 17:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:38: #2 number of paired peaks: 4120 INFO @ Sun, 21 Jun 2020 17:59:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:38: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:59:38: #2 alternative fragment length(s) may be 4,81 bps INFO @ Sun, 21 Jun 2020 17:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20_model.r INFO @ Sun, 21 Jun 2020 17:59:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.10_summits.bed INFO @ Sun, 21 Jun 2020 18:00:00: Done! pass1 - making usageList (594 chroms): 3 millis pass2 - checking and writing primary data (9434 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128303/SRX128303.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:28: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (4922 records, 4 fields): 18 millis CompletedMACS2peakCalling