Job ID = 5720649 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,364,945 reads read : 18,364,945 reads written : 18,364,945 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289746.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: 00:03:59 18364945 reads; of these: 18364945 (100.00%) were unpaired; of these: 4358931 (23.74%) aligned 0 times 11393959 (62.04%) aligned exactly 1 time 2612055 (14.22%) aligned >1 times 76.26% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 3472361 / 14006014 = 0.2479 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 00:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.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 00:54:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:45: 1000000 INFO @ Thu, 16 Apr 2020 00:54:52: 2000000 INFO @ Thu, 16 Apr 2020 00:54:58: 3000000 INFO @ Thu, 16 Apr 2020 00:55:05: 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 00:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.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 00:55:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:13: 5000000 INFO @ Thu, 16 Apr 2020 00:55:15: 1000000 INFO @ Thu, 16 Apr 2020 00:55:21: 6000000 INFO @ Thu, 16 Apr 2020 00:55:23: 2000000 INFO @ Thu, 16 Apr 2020 00:55:29: 7000000 INFO @ Thu, 16 Apr 2020 00:55:30: 3000000 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 00:55:36: 8000000 INFO @ Thu, 16 Apr 2020 00:55:37: 4000000 INFO @ Thu, 16 Apr 2020 00:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.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 00:55:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:44: 9000000 INFO @ Thu, 16 Apr 2020 00:55:45: 5000000 INFO @ Thu, 16 Apr 2020 00:55:45: 1000000 INFO @ Thu, 16 Apr 2020 00:55:52: 6000000 INFO @ Thu, 16 Apr 2020 00:55:52: 10000000 INFO @ Thu, 16 Apr 2020 00:55:53: 2000000 INFO @ Thu, 16 Apr 2020 00:55:56: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:56: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:56: #1 total tags in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:55:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:56: #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 00:55:57: #1 tags after filtering in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:57: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:58: #2 number of paired peaks: 7127 INFO @ Thu, 16 Apr 2020 00:55:58: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:58: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:58: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:58: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:58: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:55:58: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 00:55:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05_model.r INFO @ Thu, 16 Apr 2020 00:55:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:00: 7000000 INFO @ Thu, 16 Apr 2020 00:56:00: 3000000 INFO @ Thu, 16 Apr 2020 00:56:07: 8000000 INFO @ Thu, 16 Apr 2020 00:56:08: 4000000 INFO @ Thu, 16 Apr 2020 00:56:14: 9000000 INFO @ Thu, 16 Apr 2020 00:56:15: 5000000 INFO @ Thu, 16 Apr 2020 00:56:21: 10000000 INFO @ Thu, 16 Apr 2020 00:56:22: 6000000 INFO @ Thu, 16 Apr 2020 00:56:25: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:25: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:25: #1 total tags in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:56:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:25: #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 00:56:25: #1 tags after filtering in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:25: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:26: #2 number of paired peaks: 7127 INFO @ Thu, 16 Apr 2020 00:56:26: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:26: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:26: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:26: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:26: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:56:26: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 00:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10_model.r INFO @ Thu, 16 Apr 2020 00:56:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:28: 7000000 INFO @ Thu, 16 Apr 2020 00:56:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:35: 8000000 INFO @ Thu, 16 Apr 2020 00:56:41: 9000000 INFO @ Thu, 16 Apr 2020 00:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10910 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:47: 10000000 INFO @ Thu, 16 Apr 2020 00:56:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:51: #1 total tags in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:56:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:51: #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 00:56:51: #1 tags after filtering in treatment: 10533653 INFO @ Thu, 16 Apr 2020 00:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:52: #2 number of paired peaks: 7127 INFO @ Thu, 16 Apr 2020 00:56:52: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:52: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:52: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:52: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:52: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:56:52: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 00:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20_model.r INFO @ Thu, 16 Apr 2020 00:56:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8065 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592469/SRX2592469.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5438 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。