Job ID = 5720388 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,124,130 reads read : 18,124,130 reads written : 18,124,130 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289662.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:10 18124130 reads; of these: 18124130 (100.00%) were unpaired; of these: 1226815 (6.77%) aligned 0 times 13083803 (72.19%) aligned exactly 1 time 3813512 (21.04%) aligned >1 times 93.23% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4647082 / 16897315 = 0.2750 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 00:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.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 00:26:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:26:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:26:25: 1000000 INFO @ Thu, 16 Apr 2020 00:26:32: 2000000 INFO @ Thu, 16 Apr 2020 00:26:38: 3000000 INFO @ Thu, 16 Apr 2020 00:26:44: 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 @ Thu, 16 Apr 2020 00:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.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 00:26:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:26:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:26:50: 5000000 INFO @ Thu, 16 Apr 2020 00:26:55: 1000000 INFO @ Thu, 16 Apr 2020 00:26:57: 6000000 INFO @ Thu, 16 Apr 2020 00:27:02: 2000000 INFO @ Thu, 16 Apr 2020 00:27:04: 7000000 INFO @ Thu, 16 Apr 2020 00:27:09: 3000000 INFO @ Thu, 16 Apr 2020 00:27:10: 8000000 INFO @ Thu, 16 Apr 2020 00:27:15: 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 @ Thu, 16 Apr 2020 00:27:17: 9000000 INFO @ Thu, 16 Apr 2020 00:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.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 00:27:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:27:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:27:22: 5000000 INFO @ Thu, 16 Apr 2020 00:27:24: 10000000 INFO @ Thu, 16 Apr 2020 00:27:25: 1000000 INFO @ Thu, 16 Apr 2020 00:27:28: 6000000 INFO @ Thu, 16 Apr 2020 00:27:31: 11000000 INFO @ Thu, 16 Apr 2020 00:27:32: 2000000 INFO @ Thu, 16 Apr 2020 00:27:35: 7000000 INFO @ Thu, 16 Apr 2020 00:27:37: 12000000 INFO @ Thu, 16 Apr 2020 00:27:38: 3000000 INFO @ Thu, 16 Apr 2020 00:27:39: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:27:39: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:27:39: #1 total tags in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:27:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:27:39: #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 00:27:39: #1 tags after filtering in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:27:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:27:39: #1 finished! INFO @ Thu, 16 Apr 2020 00:27:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:27:40: #2 number of paired peaks: 1833 INFO @ Thu, 16 Apr 2020 00:27:40: start model_add_line... INFO @ Thu, 16 Apr 2020 00:27:40: start X-correlation... INFO @ Thu, 16 Apr 2020 00:27:41: end of X-cor INFO @ Thu, 16 Apr 2020 00:27:41: #2 finished! INFO @ Thu, 16 Apr 2020 00:27:41: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:27:41: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05_model.r INFO @ Thu, 16 Apr 2020 00:27:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:27:42: 8000000 INFO @ Thu, 16 Apr 2020 00:27:45: 4000000 INFO @ Thu, 16 Apr 2020 00:27:48: 9000000 INFO @ Thu, 16 Apr 2020 00:27:51: 5000000 INFO @ Thu, 16 Apr 2020 00:27:54: 10000000 INFO @ Thu, 16 Apr 2020 00:27:57: 6000000 INFO @ Thu, 16 Apr 2020 00:28:01: 11000000 INFO @ Thu, 16 Apr 2020 00:28:04: 7000000 INFO @ Thu, 16 Apr 2020 00:28:07: 12000000 INFO @ Thu, 16 Apr 2020 00:28:09: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:28:09: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:28:09: #1 total tags in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:28:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:28:09: #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 00:28:09: #1 tags after filtering in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:28:09: #1 finished! INFO @ Thu, 16 Apr 2020 00:28:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:28:10: 8000000 INFO @ Thu, 16 Apr 2020 00:28:10: #2 number of paired peaks: 1833 INFO @ Thu, 16 Apr 2020 00:28:10: start model_add_line... INFO @ Thu, 16 Apr 2020 00:28:10: start X-correlation... INFO @ Thu, 16 Apr 2020 00:28:10: end of X-cor INFO @ Thu, 16 Apr 2020 00:28:10: #2 finished! INFO @ Thu, 16 Apr 2020 00:28:10: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:28:10: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10_model.r INFO @ Thu, 16 Apr 2020 00:28:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:28:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:28:16: 9000000 INFO @ Thu, 16 Apr 2020 00:28:22: 10000000 INFO @ Thu, 16 Apr 2020 00:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.05_summits.bed INFO @ Thu, 16 Apr 2020 00:28:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10233 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:28:28: 11000000 INFO @ Thu, 16 Apr 2020 00:28:34: 12000000 INFO @ Thu, 16 Apr 2020 00:28:36: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:28:36: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:28:36: #1 total tags in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:28:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:28:36: #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 00:28:36: #1 tags after filtering in treatment: 12250233 INFO @ Thu, 16 Apr 2020 00:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:28:36: #1 finished! INFO @ Thu, 16 Apr 2020 00:28:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:28:37: #2 number of paired peaks: 1833 INFO @ Thu, 16 Apr 2020 00:28:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:28:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:28:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:28:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:28:37: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 00:28:37: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 00:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20_model.r INFO @ Thu, 16 Apr 2020 00:28:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:28:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:28:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:28:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:28:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.10_summits.bed INFO @ Thu, 16 Apr 2020 00:28:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7259 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:29:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592385/SRX2592385.20_summits.bed INFO @ Thu, 16 Apr 2020 00:29:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3589 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。