Job ID = 5720653 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,466,935 reads read : 15,466,935 reads written : 15,466,935 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289750.sra.cache’: No such file or directory 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: 00:03:19 15466935 reads; of these: 15466935 (100.00%) were unpaired; of these: 4708082 (30.44%) aligned 0 times 8693541 (56.21%) aligned exactly 1 time 2065312 (13.35%) aligned >1 times 69.56% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2762536 / 10758853 = 0.2568 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 @ Thu, 16 Apr 2020 00:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.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 @ Thu, 16 Apr 2020 00:53:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:58: 1000000 INFO @ Thu, 16 Apr 2020 00:54:03: 2000000 INFO @ Thu, 16 Apr 2020 00:54:08: 3000000 INFO @ Thu, 16 Apr 2020 00:54:13: 4000000 INFO @ Thu, 16 Apr 2020 00:54:18: 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 @ Thu, 16 Apr 2020 00:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.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 @ Thu, 16 Apr 2020 00:54:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:23: 6000000 INFO @ Thu, 16 Apr 2020 00:54:28: 1000000 INFO @ Thu, 16 Apr 2020 00:54:29: 7000000 INFO @ Thu, 16 Apr 2020 00:54:33: 2000000 INFO @ Thu, 16 Apr 2020 00:54:34: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:34: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:34: #1 total tags in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:54:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:54:34: #1 tags after filtering in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:34: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:35: #2 number of paired peaks: 7587 INFO @ Thu, 16 Apr 2020 00:54:35: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:35: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:35: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:35: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:35: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 00:54:35: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 00:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05_model.r INFO @ Thu, 16 Apr 2020 00:54:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:39: 3000000 INFO @ Thu, 16 Apr 2020 00:54:44: 4000000 INFO @ Thu, 16 Apr 2020 00:54:49: 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 @ Thu, 16 Apr 2020 00:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.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 @ Thu, 16 Apr 2020 00:54:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:54: 6000000 INFO @ Thu, 16 Apr 2020 00:54:59: 1000000 INFO @ Thu, 16 Apr 2020 00:55:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:00: 7000000 INFO @ Thu, 16 Apr 2020 00:55:06: 2000000 INFO @ Thu, 16 Apr 2020 00:55:06: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:06: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:06: #1 total tags in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:55:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:55:06: #1 tags after filtering in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:06: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:07: #2 number of paired peaks: 7587 INFO @ Thu, 16 Apr 2020 00:55:07: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:07: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:07: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:07: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:07: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 00:55:07: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 00:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10_model.r INFO @ Thu, 16 Apr 2020 00:55:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.05_summits.bed INFO @ Thu, 16 Apr 2020 00:55:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9515 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:12: 3000000 INFO @ Thu, 16 Apr 2020 00:55:19: 4000000 INFO @ Thu, 16 Apr 2020 00:55:25: 5000000 INFO @ Thu, 16 Apr 2020 00:55:31: 6000000 INFO @ Thu, 16 Apr 2020 00:55:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:37: 7000000 INFO @ Thu, 16 Apr 2020 00:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.10_summits.bed INFO @ Thu, 16 Apr 2020 00:55:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7558 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:43: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:43: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:43: #1 total tags in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:55:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:55:43: #1 tags after filtering in treatment: 7996317 INFO @ Thu, 16 Apr 2020 00:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:44: #2 number of paired peaks: 7587 INFO @ Thu, 16 Apr 2020 00:55:44: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:44: #2 predicted fragment length is 193 bps INFO @ Thu, 16 Apr 2020 00:55:44: #2 alternative fragment length(s) may be 193 bps INFO @ Thu, 16 Apr 2020 00:55:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20_model.r INFO @ Thu, 16 Apr 2020 00:55:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592473/SRX2592473.20_summits.bed INFO @ Thu, 16 Apr 2020 00:56:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5626 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。