Job ID = 5720586 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,734,283 reads read : 12,734,283 reads written : 12,734,283 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289715.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: 00:03:33 12734283 reads; of these: 12734283 (100.00%) were unpaired; of these: 1164783 (9.15%) aligned 0 times 9715529 (76.29%) aligned exactly 1 time 1853971 (14.56%) aligned >1 times 90.85% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 2335450 / 11569500 = 0.2019 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 00:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.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 00:42:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:42:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:42:38: 1000000 INFO @ Thu, 16 Apr 2020 00:42:43: 2000000 INFO @ Thu, 16 Apr 2020 00:42:49: 3000000 INFO @ Thu, 16 Apr 2020 00:42:55: 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 @ Thu, 16 Apr 2020 00:43:00: 5000000 INFO @ Thu, 16 Apr 2020 00:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.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 00:43:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:07: 6000000 INFO @ Thu, 16 Apr 2020 00:43:09: 1000000 INFO @ Thu, 16 Apr 2020 00:43:14: 7000000 INFO @ Thu, 16 Apr 2020 00:43:17: 2000000 INFO @ Thu, 16 Apr 2020 00:43:21: 8000000 INFO @ Thu, 16 Apr 2020 00:43:25: 3000000 INFO @ Thu, 16 Apr 2020 00:43:28: 9000000 INFO @ Thu, 16 Apr 2020 00:43:29: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:43:29: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:43:29: #1 total tags in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:43:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:29: #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 00:43:29: #1 tags after filtering in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:43:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:29: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:29: #2 looking for paired plus/minus strand peaks... 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 00:43:30: #2 number of paired peaks: 1386 INFO @ Thu, 16 Apr 2020 00:43:30: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:30: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:30: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:30: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:30: #2 predicted fragment length is 246 bps INFO @ Thu, 16 Apr 2020 00:43:30: #2 alternative fragment length(s) may be 246 bps INFO @ Thu, 16 Apr 2020 00:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05_model.r INFO @ Thu, 16 Apr 2020 00:43:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.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 00:43:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:32: 4000000 INFO @ Thu, 16 Apr 2020 00:43:39: 1000000 INFO @ Thu, 16 Apr 2020 00:43:40: 5000000 INFO @ Thu, 16 Apr 2020 00:43:47: 2000000 INFO @ Thu, 16 Apr 2020 00:43:47: 6000000 INFO @ Thu, 16 Apr 2020 00:43:54: 3000000 INFO @ Thu, 16 Apr 2020 00:43:55: 7000000 INFO @ Thu, 16 Apr 2020 00:43:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:01: 4000000 INFO @ Thu, 16 Apr 2020 00:44:02: 8000000 INFO @ Thu, 16 Apr 2020 00:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.05_summits.bed INFO @ Thu, 16 Apr 2020 00:44:08: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (16001 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:44:09: 5000000 INFO @ Thu, 16 Apr 2020 00:44:10: 9000000 INFO @ Thu, 16 Apr 2020 00:44:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:44:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:44:12: #1 total tags in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:44:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:12: #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 00:44:12: #1 tags after filtering in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:13: #2 number of paired peaks: 1386 INFO @ Thu, 16 Apr 2020 00:44:13: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:13: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:13: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:13: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:13: #2 predicted fragment length is 246 bps INFO @ Thu, 16 Apr 2020 00:44:13: #2 alternative fragment length(s) may be 246 bps INFO @ Thu, 16 Apr 2020 00:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10_model.r INFO @ Thu, 16 Apr 2020 00:44:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:44:16: 6000000 INFO @ Thu, 16 Apr 2020 00:44:23: 7000000 INFO @ Thu, 16 Apr 2020 00:44:30: 8000000 INFO @ Thu, 16 Apr 2020 00:44:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:44:37: 9000000 INFO @ Thu, 16 Apr 2020 00:44:39: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:44:39: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:44:39: #1 total tags in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:44:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:39: #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 00:44:39: #1 tags after filtering in treatment: 9234050 INFO @ Thu, 16 Apr 2020 00:44:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:39: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:40: #2 number of paired peaks: 1386 INFO @ Thu, 16 Apr 2020 00:44:40: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:40: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:40: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:40: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:40: #2 predicted fragment length is 246 bps INFO @ Thu, 16 Apr 2020 00:44:40: #2 alternative fragment length(s) may be 246 bps INFO @ Thu, 16 Apr 2020 00:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20_model.r INFO @ Thu, 16 Apr 2020 00:44:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.10_summits.bed INFO @ Thu, 16 Apr 2020 00:44:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10259 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:45:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592438/SRX2592438.20_summits.bed INFO @ Thu, 16 Apr 2020 00:45:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4653 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。