Job ID = 5720694 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,890,062 reads read : 10,890,062 reads written : 10,890,062 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR7148579.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: 00:02:57 10890062 reads; of these: 10890062 (100.00%) were unpaired; of these: 517277 (4.75%) aligned 0 times 8464652 (77.73%) aligned exactly 1 time 1908133 (17.52%) aligned >1 times 95.25% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 1086157 / 10372785 = 0.1047 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 01:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.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 01:01:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:41: 1000000 INFO @ Thu, 16 Apr 2020 01:01:47: 2000000 INFO @ Thu, 16 Apr 2020 01:01:52: 3000000 INFO @ Thu, 16 Apr 2020 01:01:58: 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 01:02:03: 5000000 INFO @ Thu, 16 Apr 2020 01:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.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 01:02:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:02:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:02:09: 6000000 INFO @ Thu, 16 Apr 2020 01:02:11: 1000000 INFO @ Thu, 16 Apr 2020 01:02:15: 7000000 INFO @ Thu, 16 Apr 2020 01:02:17: 2000000 INFO @ Thu, 16 Apr 2020 01:02:20: 8000000 INFO @ Thu, 16 Apr 2020 01:02:23: 3000000 INFO @ Thu, 16 Apr 2020 01:02:26: 9000000 INFO @ Thu, 16 Apr 2020 01:02:28: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:02:28: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:02:28: #1 total tags in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:02:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:28: #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 01:02:28: #1 tags after filtering in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:28: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:28: 4000000 INFO @ Thu, 16 Apr 2020 01:02:29: #2 number of paired peaks: 1737 INFO @ Thu, 16 Apr 2020 01:02:29: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:29: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:29: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:29: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:29: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 01:02:29: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 01:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05_model.r INFO @ Thu, 16 Apr 2020 01:02:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:29: #3 Pre-compute pvalue-qvalue table... 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 01:02:34: 5000000 INFO @ Thu, 16 Apr 2020 01:02:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.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 01:02:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:02:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:02:40: 6000000 INFO @ Thu, 16 Apr 2020 01:02:41: 1000000 INFO @ Thu, 16 Apr 2020 01:02:46: 7000000 INFO @ Thu, 16 Apr 2020 01:02:47: 2000000 INFO @ Thu, 16 Apr 2020 01:02:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:52: 8000000 INFO @ Thu, 16 Apr 2020 01:02:53: 3000000 INFO @ Thu, 16 Apr 2020 01:02:58: 9000000 INFO @ Thu, 16 Apr 2020 01:02:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.05_summits.bed INFO @ Thu, 16 Apr 2020 01:02:59: Done! INFO @ Thu, 16 Apr 2020 01:02:59: 4000000 INFO @ Thu, 16 Apr 2020 01:02:59: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:02:59: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:02:59: #1 total tags in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:02:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:59: #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 01:02:59: #1 tags after filtering in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:59: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:03:00: #2 number of paired peaks: 1737 INFO @ Thu, 16 Apr 2020 01:03:00: start model_add_line... INFO @ Thu, 16 Apr 2020 01:03:00: start X-correlation... INFO @ Thu, 16 Apr 2020 01:03:00: end of X-cor INFO @ Thu, 16 Apr 2020 01:03:00: #2 finished! INFO @ Thu, 16 Apr 2020 01:03:00: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 01:03:00: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 01:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10_model.r INFO @ Thu, 16 Apr 2020 01:03:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:03:00: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6292 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:05: 5000000 INFO @ Thu, 16 Apr 2020 01:03:10: 6000000 INFO @ Thu, 16 Apr 2020 01:03:16: 7000000 INFO @ Thu, 16 Apr 2020 01:03:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:21: 8000000 INFO @ Thu, 16 Apr 2020 01:03:27: 9000000 INFO @ Thu, 16 Apr 2020 01:03:29: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:03:29: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:03:29: #1 total tags in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:03:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:03:29: #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 01:03:29: #1 tags after filtering in treatment: 9286628 INFO @ Thu, 16 Apr 2020 01:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:03:29: #1 finished! INFO @ Thu, 16 Apr 2020 01:03:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:03:30: #2 number of paired peaks: 1737 INFO @ Thu, 16 Apr 2020 01:03:30: start model_add_line... INFO @ Thu, 16 Apr 2020 01:03:30: start X-correlation... INFO @ Thu, 16 Apr 2020 01:03:30: end of X-cor INFO @ Thu, 16 Apr 2020 01:03:30: #2 finished! INFO @ Thu, 16 Apr 2020 01:03:30: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 01:03:30: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 01:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20_model.r INFO @ Thu, 16 Apr 2020 01:03:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.10_summits.bed INFO @ Thu, 16 Apr 2020 01:03:30: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3498 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068068/SRX4068068.20_summits.bed INFO @ Thu, 16 Apr 2020 01:03:59: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1426 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。