Job ID = 5720704 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,408,371 reads read : 3,408,371 reads written : 3,408,371 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: 00:00:46 3408371 reads; of these: 3408371 (100.00%) were unpaired; of these: 76065 (2.23%) aligned 0 times 3007191 (88.23%) aligned exactly 1 time 325115 (9.54%) aligned >1 times 97.77% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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_rmdupse_core] 119344 / 3332306 = 0.0358 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 01:03:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.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 01:03:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:03:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:03:49: 1000000 INFO @ Thu, 16 Apr 2020 01:03:56: 2000000 INFO @ Thu, 16 Apr 2020 01:04:02: 3000000 INFO @ Thu, 16 Apr 2020 01:04:04: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:04:04: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:04:04: #1 total tags in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:04:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:04:04: #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 01:04:04: #1 tags after filtering in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:04:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:04:04: #1 finished! INFO @ Thu, 16 Apr 2020 01:04:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:04:04: #2 number of paired peaks: 7460 INFO @ Thu, 16 Apr 2020 01:04:04: start model_add_line... INFO @ Thu, 16 Apr 2020 01:04:04: start X-correlation... INFO @ Thu, 16 Apr 2020 01:04:04: end of X-cor INFO @ Thu, 16 Apr 2020 01:04:04: #2 finished! INFO @ Thu, 16 Apr 2020 01:04:04: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 01:04:04: #2 alternative fragment length(s) may be 4,145 bps INFO @ Thu, 16 Apr 2020 01:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05_model.r INFO @ Thu, 16 Apr 2020 01:04:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:04:11: #3 Call peaks for each chromosome... 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 01:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.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 01:04:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:04:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.05_summits.bed INFO @ Thu, 16 Apr 2020 01:04:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2779 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:04:19: 1000000 INFO @ Thu, 16 Apr 2020 01:04:25: 2000000 INFO @ Thu, 16 Apr 2020 01:04:31: 3000000 INFO @ Thu, 16 Apr 2020 01:04:32: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:04:32: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:04:32: #1 total tags in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:04:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:04:32: #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 01:04:32: #1 tags after filtering in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:04:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:04:32: #1 finished! INFO @ Thu, 16 Apr 2020 01:04:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:04:33: #2 number of paired peaks: 7460 INFO @ Thu, 16 Apr 2020 01:04:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:04:33: start X-correlation... INFO @ Thu, 16 Apr 2020 01:04:33: end of X-cor INFO @ Thu, 16 Apr 2020 01:04:33: #2 finished! INFO @ Thu, 16 Apr 2020 01:04:33: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 01:04:33: #2 alternative fragment length(s) may be 4,145 bps INFO @ Thu, 16 Apr 2020 01:04:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10_model.r INFO @ Thu, 16 Apr 2020 01:04:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:04:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:04:40: #3 Call peaks for each chromosome... 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 01:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.10_summits.bed INFO @ Thu, 16 Apr 2020 01:04:43: Done! INFO @ Thu, 16 Apr 2020 01:04:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.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 01:04:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:04:43: #1 read treatment tags... pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (551 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:04:49: 1000000 INFO @ Thu, 16 Apr 2020 01:04:55: 2000000 INFO @ Thu, 16 Apr 2020 01:05:01: 3000000 INFO @ Thu, 16 Apr 2020 01:05:02: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:05:02: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:05:02: #1 total tags in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:05:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:05:02: #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 01:05:02: #1 tags after filtering in treatment: 3212962 INFO @ Thu, 16 Apr 2020 01:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:05:02: #1 finished! INFO @ Thu, 16 Apr 2020 01:05:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:05:03: #2 number of paired peaks: 7460 INFO @ Thu, 16 Apr 2020 01:05:03: start model_add_line... INFO @ Thu, 16 Apr 2020 01:05:03: start X-correlation... INFO @ Thu, 16 Apr 2020 01:05:03: end of X-cor INFO @ Thu, 16 Apr 2020 01:05:03: #2 finished! INFO @ Thu, 16 Apr 2020 01:05:03: #2 predicted fragment length is 145 bps INFO @ Thu, 16 Apr 2020 01:05:03: #2 alternative fragment length(s) may be 4,145 bps INFO @ Thu, 16 Apr 2020 01:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20_model.r INFO @ Thu, 16 Apr 2020 01:05:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:05:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158168/SRX4158168.20_summits.bed INFO @ Thu, 16 Apr 2020 01:05:13: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。