Job ID = 5790696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,837,522 reads read : 36,837,522 reads written : 36,837,522 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982430.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:48 36837522 reads; of these: 36837522 (100.00%) were unpaired; of these: 9146555 (24.83%) aligned 0 times 22317909 (60.58%) aligned exactly 1 time 5373058 (14.59%) aligned >1 times 75.17% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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_sort_core] merging from 8 files... [bam_rmdupse_core] 14947126 / 27690967 = 0.5398 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 06:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.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 06:25:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:25:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:25:41: 1000000 INFO @ Wed, 22 Apr 2020 06:25:46: 2000000 INFO @ Wed, 22 Apr 2020 06:25:51: 3000000 INFO @ Wed, 22 Apr 2020 06:25:55: 4000000 INFO @ Wed, 22 Apr 2020 06:26:00: 5000000 INFO @ Wed, 22 Apr 2020 06:26:05: 6000000 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 06:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.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 06:26:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:26:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:26:09: 7000000 INFO @ Wed, 22 Apr 2020 06:26:12: 1000000 INFO @ Wed, 22 Apr 2020 06:26:14: 8000000 INFO @ Wed, 22 Apr 2020 06:26:16: 2000000 INFO @ Wed, 22 Apr 2020 06:26:19: 9000000 INFO @ Wed, 22 Apr 2020 06:26:21: 3000000 INFO @ Wed, 22 Apr 2020 06:26:24: 10000000 INFO @ Wed, 22 Apr 2020 06:26:26: 4000000 INFO @ Wed, 22 Apr 2020 06:26:29: 11000000 INFO @ Wed, 22 Apr 2020 06:26:31: 5000000 INFO @ Wed, 22 Apr 2020 06:26:33: 12000000 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 06:26:36: 6000000 INFO @ Wed, 22 Apr 2020 06:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.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 06:26:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:26:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:26:37: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:26:37: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:26:37: #1 total tags in treatment: 12743841 INFO @ Wed, 22 Apr 2020 06:26:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:26:37: #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 06:26:38: #1 tags after filtering in treatment: 12743631 INFO @ Wed, 22 Apr 2020 06:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:38: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:39: #2 number of paired peaks: 22954 INFO @ Wed, 22 Apr 2020 06:26:39: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:40: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:40: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:40: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:40: #2 predicted fragment length is 219 bps INFO @ Wed, 22 Apr 2020 06:26:40: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 22 Apr 2020 06:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05_model.r INFO @ Wed, 22 Apr 2020 06:26:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:41: 7000000 INFO @ Wed, 22 Apr 2020 06:26:42: 1000000 INFO @ Wed, 22 Apr 2020 06:26:46: 8000000 INFO @ Wed, 22 Apr 2020 06:26:46: 2000000 INFO @ Wed, 22 Apr 2020 06:26:51: 9000000 INFO @ Wed, 22 Apr 2020 06:26:51: 3000000 INFO @ Wed, 22 Apr 2020 06:26:56: 10000000 INFO @ Wed, 22 Apr 2020 06:26:56: 4000000 INFO @ Wed, 22 Apr 2020 06:27:00: 11000000 INFO @ Wed, 22 Apr 2020 06:27:01: 5000000 INFO @ Wed, 22 Apr 2020 06:27:05: 12000000 INFO @ Wed, 22 Apr 2020 06:27:05: 6000000 INFO @ Wed, 22 Apr 2020 06:27:09: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:27:09: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:27:09: #1 total tags in treatment: 12743841 INFO @ Wed, 22 Apr 2020 06:27:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:27:09: #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 06:27:10: #1 tags after filtering in treatment: 12743631 INFO @ Wed, 22 Apr 2020 06:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:27:10: #1 finished! INFO @ Wed, 22 Apr 2020 06:27:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:27:10: 7000000 INFO @ Wed, 22 Apr 2020 06:27:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:11: #2 number of paired peaks: 22954 INFO @ Wed, 22 Apr 2020 06:27:11: start model_add_line... INFO @ Wed, 22 Apr 2020 06:27:11: start X-correlation... INFO @ Wed, 22 Apr 2020 06:27:11: end of X-cor INFO @ Wed, 22 Apr 2020 06:27:11: #2 finished! INFO @ Wed, 22 Apr 2020 06:27:11: #2 predicted fragment length is 219 bps INFO @ Wed, 22 Apr 2020 06:27:11: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 22 Apr 2020 06:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10_model.r INFO @ Wed, 22 Apr 2020 06:27:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:27:15: 8000000 INFO @ Wed, 22 Apr 2020 06:27:19: 9000000 INFO @ Wed, 22 Apr 2020 06:27:24: 10000000 INFO @ Wed, 22 Apr 2020 06:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.05_summits.bed INFO @ Wed, 22 Apr 2020 06:27:26: Done! pass1 - making usageList (136 chroms): 3 millis pass2 - checking and writing primary data (18027 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:27:29: 11000000 INFO @ Wed, 22 Apr 2020 06:27:33: 12000000 INFO @ Wed, 22 Apr 2020 06:27:37: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:27:37: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:27:37: #1 total tags in treatment: 12743841 INFO @ Wed, 22 Apr 2020 06:27:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:27:37: #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 06:27:37: #1 tags after filtering in treatment: 12743631 INFO @ Wed, 22 Apr 2020 06:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:27:37: #1 finished! INFO @ Wed, 22 Apr 2020 06:27:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:27:39: #2 number of paired peaks: 22954 INFO @ Wed, 22 Apr 2020 06:27:39: start model_add_line... INFO @ Wed, 22 Apr 2020 06:27:39: start X-correlation... INFO @ Wed, 22 Apr 2020 06:27:39: end of X-cor INFO @ Wed, 22 Apr 2020 06:27:39: #2 finished! INFO @ Wed, 22 Apr 2020 06:27:39: #2 predicted fragment length is 219 bps INFO @ Wed, 22 Apr 2020 06:27:39: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 22 Apr 2020 06:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20_model.r INFO @ Wed, 22 Apr 2020 06:27:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:27:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.10_summits.bed INFO @ Wed, 22 Apr 2020 06:27:59: Done! pass1 - making usageList (111 chroms): 2 millis pass2 - checking and writing primary data (15435 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:28:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761728/SRX5761728.20_summits.bed INFO @ Wed, 22 Apr 2020 06:28:24: Done! pass1 - making usageList (91 chroms): 2 millis pass2 - checking and writing primary data (12892 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。