Job ID = 5720232 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,329,835 reads read : 13,329,835 reads written : 13,329,835 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:19 13329835 reads; of these: 13329835 (100.00%) were unpaired; of these: 2769074 (20.77%) aligned 0 times 9190500 (68.95%) aligned exactly 1 time 1370261 (10.28%) aligned >1 times 79.23% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2907669 / 10560761 = 0.2753 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, 15 Apr 2020 22:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:30:57: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:30:57: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:31:03: 1000000 INFO @ Wed, 15 Apr 2020 22:31:09: 2000000 INFO @ Wed, 15 Apr 2020 22:31:14: 3000000 INFO @ Wed, 15 Apr 2020 22:31:20: 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 @ Wed, 15 Apr 2020 22:31:26: 5000000 INFO @ Wed, 15 Apr 2020 22:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:31:27: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:31:27: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:31:32: 6000000 INFO @ Wed, 15 Apr 2020 22:31:33: 1000000 INFO @ Wed, 15 Apr 2020 22:31:38: 7000000 INFO @ Wed, 15 Apr 2020 22:31:40: 2000000 INFO @ Wed, 15 Apr 2020 22:31:42: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:31:42: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:31:42: #1 total tags in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:31:42: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:31:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:31:42: #1 tags after filtering in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:31:42: #1 finished! INFO @ Wed, 15 Apr 2020 22:31:42: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:31:43: #2 number of paired peaks: 2572 INFO @ Wed, 15 Apr 2020 22:31:43: start model_add_line... INFO @ Wed, 15 Apr 2020 22:31:43: start X-correlation... INFO @ Wed, 15 Apr 2020 22:31:43: end of X-cor INFO @ Wed, 15 Apr 2020 22:31:43: #2 finished! INFO @ Wed, 15 Apr 2020 22:31:43: #2 predicted fragment length is 140 bps INFO @ Wed, 15 Apr 2020 22:31:43: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 15 Apr 2020 22:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05_model.r INFO @ Wed, 15 Apr 2020 22:31:43: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:31:46: 3000000 INFO @ Wed, 15 Apr 2020 22:31:51: 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 @ Wed, 15 Apr 2020 22:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 22:31:57: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:31:57: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:31:57: 5000000 INFO @ Wed, 15 Apr 2020 22:32:01: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:32:03: 1000000 INFO @ Wed, 15 Apr 2020 22:32:04: 6000000 INFO @ Wed, 15 Apr 2020 22:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:32:09: 2000000 INFO @ Wed, 15 Apr 2020 22:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.05_summits.bed INFO @ Wed, 15 Apr 2020 22:32:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6018 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:32:10: 7000000 INFO @ Wed, 15 Apr 2020 22:32:14: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:32:14: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:32:14: #1 total tags in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:32:14: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:32:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:32:14: #1 tags after filtering in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:32:14: #1 finished! INFO @ Wed, 15 Apr 2020 22:32:14: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:32:15: #2 number of paired peaks: 2572 INFO @ Wed, 15 Apr 2020 22:32:15: start model_add_line... INFO @ Wed, 15 Apr 2020 22:32:15: start X-correlation... INFO @ Wed, 15 Apr 2020 22:32:15: end of X-cor INFO @ Wed, 15 Apr 2020 22:32:15: #2 finished! INFO @ Wed, 15 Apr 2020 22:32:15: #2 predicted fragment length is 140 bps INFO @ Wed, 15 Apr 2020 22:32:15: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 15 Apr 2020 22:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10_model.r INFO @ Wed, 15 Apr 2020 22:32:15: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:32:15: 3000000 INFO @ Wed, 15 Apr 2020 22:32:21: 4000000 INFO @ Wed, 15 Apr 2020 22:32:27: 5000000 INFO @ Wed, 15 Apr 2020 22:32:33: 6000000 INFO @ Wed, 15 Apr 2020 22:32:35: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:32:39: 7000000 INFO @ Wed, 15 Apr 2020 22:32:43: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:32:43: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:32:43: #1 total tags in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:32:43: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:32:43: #1 tags after filtering in treatment: 7653092 INFO @ Wed, 15 Apr 2020 22:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:32:43: #1 finished! INFO @ Wed, 15 Apr 2020 22:32:43: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:32:44: #2 number of paired peaks: 2572 INFO @ Wed, 15 Apr 2020 22:32:44: start model_add_line... INFO @ Wed, 15 Apr 2020 22:32:44: start X-correlation... INFO @ Wed, 15 Apr 2020 22:32:44: end of X-cor INFO @ Wed, 15 Apr 2020 22:32:44: #2 finished! INFO @ Wed, 15 Apr 2020 22:32:44: #2 predicted fragment length is 140 bps INFO @ Wed, 15 Apr 2020 22:32:44: #2 alternative fragment length(s) may be 140 bps INFO @ Wed, 15 Apr 2020 22:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20_model.r INFO @ Wed, 15 Apr 2020 22:32:44: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:32:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.10_summits.bed INFO @ Wed, 15 Apr 2020 22:32:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3614 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:33:03: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720161/SRX6720161.20_summits.bed INFO @ Wed, 15 Apr 2020 22:33:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。