Job ID = 5790791 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 237,871 reads read : 475,742 reads written : 237,871 reads 0-length : 237,871 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: 00:00:02 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:14 237871 reads; of these: 237871 (100.00%) were unpaired; of these: 70892 (29.80%) aligned 0 times 117023 (49.20%) aligned exactly 1 time 49956 (21.00%) aligned >1 times 70.20% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 5085 / 166979 = 0.0305 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 07:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.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 07:18:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:18:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:18:28: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:18:28: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:18:28: #1 total tags in treatment: 161894 INFO @ Wed, 22 Apr 2020 07:18:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:18:28: #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 07:18:28: #1 tags after filtering in treatment: 161722 INFO @ Wed, 22 Apr 2020 07:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:18:28: #1 finished! INFO @ Wed, 22 Apr 2020 07:18:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:18:29: #2 number of paired peaks: 1604 INFO @ Wed, 22 Apr 2020 07:18:29: start model_add_line... INFO @ Wed, 22 Apr 2020 07:18:29: start X-correlation... INFO @ Wed, 22 Apr 2020 07:18:29: end of X-cor INFO @ Wed, 22 Apr 2020 07:18:29: #2 finished! INFO @ Wed, 22 Apr 2020 07:18:29: #2 predicted fragment length is 302 bps INFO @ Wed, 22 Apr 2020 07:18:29: #2 alternative fragment length(s) may be 302 bps INFO @ Wed, 22 Apr 2020 07:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05_model.r INFO @ Wed, 22 Apr 2020 07:18:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:18:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.05_summits.bed INFO @ Wed, 22 Apr 2020 07:18:29: Done! pass1 - making usageList (20 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.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 07:18:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:18:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:18:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:18:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:18:58: #1 total tags in treatment: 161894 INFO @ Wed, 22 Apr 2020 07:18:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:18:58: #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 07:18:58: #1 tags after filtering in treatment: 161722 INFO @ Wed, 22 Apr 2020 07:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:18:58: #1 finished! INFO @ Wed, 22 Apr 2020 07:18:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:18:59: #2 number of paired peaks: 1604 INFO @ Wed, 22 Apr 2020 07:18:59: start model_add_line... INFO @ Wed, 22 Apr 2020 07:18:59: start X-correlation... INFO @ Wed, 22 Apr 2020 07:18:59: end of X-cor INFO @ Wed, 22 Apr 2020 07:18:59: #2 finished! INFO @ Wed, 22 Apr 2020 07:18:59: #2 predicted fragment length is 302 bps INFO @ Wed, 22 Apr 2020 07:18:59: #2 alternative fragment length(s) may be 302 bps INFO @ Wed, 22 Apr 2020 07:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10_model.r INFO @ Wed, 22 Apr 2020 07:18:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:18:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:19:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:19:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:19:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.10_summits.bed INFO @ Wed, 22 Apr 2020 07:19:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.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 07:19:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:19:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:19:27: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:19:27: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:19:27: #1 total tags in treatment: 161894 INFO @ Wed, 22 Apr 2020 07:19:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:19:27: #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 07:19:27: #1 tags after filtering in treatment: 161722 INFO @ Wed, 22 Apr 2020 07:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:19:27: #1 finished! INFO @ Wed, 22 Apr 2020 07:19:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:19:28: #2 number of paired peaks: 1604 INFO @ Wed, 22 Apr 2020 07:19:28: start model_add_line... INFO @ Wed, 22 Apr 2020 07:19:28: start X-correlation... INFO @ Wed, 22 Apr 2020 07:19:28: end of X-cor INFO @ Wed, 22 Apr 2020 07:19:28: #2 finished! INFO @ Wed, 22 Apr 2020 07:19:28: #2 predicted fragment length is 302 bps INFO @ Wed, 22 Apr 2020 07:19:28: #2 alternative fragment length(s) may be 302 bps INFO @ Wed, 22 Apr 2020 07:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20_model.r INFO @ Wed, 22 Apr 2020 07:19:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:19:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625160/SRX7625160.20_summits.bed INFO @ Wed, 22 Apr 2020 07:19:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。