Job ID = 5790711 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,075,334 reads read : 21,075,334 reads written : 21,075,334 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:55 21075334 reads; of these: 21075334 (100.00%) were unpaired; of these: 5165246 (24.51%) aligned 0 times 12125203 (57.53%) aligned exactly 1 time 3784885 (17.96%) aligned >1 times 75.49% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 2690739 / 15910088 = 0.1691 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 @ Wed, 22 Apr 2020 06:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:41:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:41:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:41:47: 1000000 INFO @ Wed, 22 Apr 2020 06:41:52: 2000000 INFO @ Wed, 22 Apr 2020 06:41:57: 3000000 INFO @ Wed, 22 Apr 2020 06:42:02: 4000000 INFO @ Wed, 22 Apr 2020 06:42:07: 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 @ Wed, 22 Apr 2020 06:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:42:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:42:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:42:13: 6000000 INFO @ Wed, 22 Apr 2020 06:42:17: 1000000 INFO @ Wed, 22 Apr 2020 06:42:19: 7000000 INFO @ Wed, 22 Apr 2020 06:42:23: 2000000 INFO @ Wed, 22 Apr 2020 06:42:25: 8000000 INFO @ Wed, 22 Apr 2020 06:42:29: 3000000 INFO @ Wed, 22 Apr 2020 06:42:31: 9000000 INFO @ Wed, 22 Apr 2020 06:42:35: 4000000 INFO @ Wed, 22 Apr 2020 06:42:37: 10000000 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 @ Wed, 22 Apr 2020 06:42:41: 5000000 INFO @ Wed, 22 Apr 2020 06:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:42:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:42:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:42:43: 11000000 INFO @ Wed, 22 Apr 2020 06:42:47: 6000000 INFO @ Wed, 22 Apr 2020 06:42:47: 1000000 INFO @ Wed, 22 Apr 2020 06:42:49: 12000000 INFO @ Wed, 22 Apr 2020 06:42:53: 7000000 INFO @ Wed, 22 Apr 2020 06:42:53: 2000000 INFO @ Wed, 22 Apr 2020 06:42:55: 13000000 INFO @ Wed, 22 Apr 2020 06:42:56: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:42:56: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:42:56: #1 total tags in treatment: 13219349 INFO @ Wed, 22 Apr 2020 06:42:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:42:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:42:56: #1 tags after filtering in treatment: 13219128 INFO @ Wed, 22 Apr 2020 06:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:42:56: #1 finished! INFO @ Wed, 22 Apr 2020 06:42:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:42:59: 8000000 INFO @ Wed, 22 Apr 2020 06:42:59: #2 number of paired peaks: 48600 INFO @ Wed, 22 Apr 2020 06:42:59: start model_add_line... INFO @ Wed, 22 Apr 2020 06:42:59: start X-correlation... INFO @ Wed, 22 Apr 2020 06:42:59: end of X-cor INFO @ Wed, 22 Apr 2020 06:42:59: #2 finished! INFO @ Wed, 22 Apr 2020 06:42:59: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:42:59: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:42:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05_model.r INFO @ Wed, 22 Apr 2020 06:42:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:42:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:42:59: 3000000 INFO @ Wed, 22 Apr 2020 06:43:04: 9000000 INFO @ Wed, 22 Apr 2020 06:43:05: 4000000 INFO @ Wed, 22 Apr 2020 06:43:10: 10000000 INFO @ Wed, 22 Apr 2020 06:43:11: 5000000 INFO @ Wed, 22 Apr 2020 06:43:16: 11000000 INFO @ Wed, 22 Apr 2020 06:43:17: 6000000 INFO @ Wed, 22 Apr 2020 06:43:22: 12000000 INFO @ Wed, 22 Apr 2020 06:43:23: 7000000 INFO @ Wed, 22 Apr 2020 06:43:28: 13000000 INFO @ Wed, 22 Apr 2020 06:43:29: 8000000 INFO @ Wed, 22 Apr 2020 06:43:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:43:29: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:43:29: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:43:29: #1 total tags in treatment: 13219349 INFO @ Wed, 22 Apr 2020 06:43:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:43:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:43:30: #1 tags after filtering in treatment: 13219128 INFO @ Wed, 22 Apr 2020 06:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:43:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:43:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:43:32: #2 number of paired peaks: 48600 INFO @ Wed, 22 Apr 2020 06:43:32: start model_add_line... INFO @ Wed, 22 Apr 2020 06:43:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:43:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:43:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:43:32: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:43:32: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10_model.r INFO @ Wed, 22 Apr 2020 06:43:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:43:34: 9000000 INFO @ Wed, 22 Apr 2020 06:43:39: 10000000 INFO @ Wed, 22 Apr 2020 06:43:44: 11000000 INFO @ Wed, 22 Apr 2020 06:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.05_summits.bed INFO @ Wed, 22 Apr 2020 06:43:45: Done! pass1 - making usageList (93 chroms): 3 millis pass2 - checking and writing primary data (12190 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:43:50: 12000000 INFO @ Wed, 22 Apr 2020 06:43:55: 13000000 INFO @ Wed, 22 Apr 2020 06:43:56: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:43:56: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:43:56: #1 total tags in treatment: 13219349 INFO @ Wed, 22 Apr 2020 06:43:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:43:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:43:57: #1 tags after filtering in treatment: 13219128 INFO @ Wed, 22 Apr 2020 06:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:43:57: #1 finished! INFO @ Wed, 22 Apr 2020 06:43:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:43:59: #2 number of paired peaks: 48600 INFO @ Wed, 22 Apr 2020 06:43:59: start model_add_line... INFO @ Wed, 22 Apr 2020 06:43:59: start X-correlation... INFO @ Wed, 22 Apr 2020 06:43:59: end of X-cor INFO @ Wed, 22 Apr 2020 06:43:59: #2 finished! INFO @ Wed, 22 Apr 2020 06:43:59: #2 predicted fragment length is 237 bps INFO @ Wed, 22 Apr 2020 06:43:59: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 22 Apr 2020 06:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20_model.r INFO @ Wed, 22 Apr 2020 06:43:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:44:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.10_summits.bed INFO @ Wed, 22 Apr 2020 06:44:19: Done! pass1 - making usageList (76 chroms): 2 millis pass2 - checking and writing primary data (9286 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:44:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761741/SRX5761741.20_summits.bed INFO @ Wed, 22 Apr 2020 06:44:46: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (6949 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。