Job ID = 6366636 SRX = SRX2144183 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:15 prefetch.2.10.7: 1) Downloading 'SRR4188787'... 2020-06-15T22:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:00 prefetch.2.10.7: 'SRR4188787' is valid 2020-06-15T22:55:00 prefetch.2.10.7: 1) 'SRR4188787' was downloaded successfully Read 6715360 spots for SRR4188787/SRR4188787.sra Written 6715360 spots for SRR4188787/SRR4188787.sra 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: 00:01:21 6715360 reads; of these: 6715360 (100.00%) were unpaired; of these: 1188402 (17.70%) aligned 0 times 4685816 (69.78%) aligned exactly 1 time 841142 (12.53%) aligned >1 times 82.30% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1402121 / 5526958 = 0.2537 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 @ Tue, 16 Jun 2020 07:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:58:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:40: 1000000 INFO @ Tue, 16 Jun 2020 07:58:46: 2000000 INFO @ Tue, 16 Jun 2020 07:58:51: 3000000 INFO @ Tue, 16 Jun 2020 07:58:57: 4000000 INFO @ Tue, 16 Jun 2020 07:58:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:58:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:58:57: #1 total tags in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:58:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:58:57: #1 tags after filtering in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:58: #2 number of paired peaks: 1543 INFO @ Tue, 16 Jun 2020 07:58:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:58: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:58:58: #2 alternative fragment length(s) may be 4,124 bps INFO @ Tue, 16 Jun 2020 07:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05_model.r INFO @ Tue, 16 Jun 2020 07:58:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:58: #3 Pre-compute pvalue-qvalue table... 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 @ Tue, 16 Jun 2020 07:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:59:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:10: 1000000 INFO @ Tue, 16 Jun 2020 07:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.05_summits.bed INFO @ Tue, 16 Jun 2020 07:59:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1621 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:15: 2000000 INFO @ Tue, 16 Jun 2020 07:59:20: 3000000 INFO @ Tue, 16 Jun 2020 07:59:25: 4000000 INFO @ Tue, 16 Jun 2020 07:59:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:59:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:59:25: #1 total tags in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:59:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:59:26: #1 tags after filtering in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:26: #2 number of paired peaks: 1543 INFO @ Tue, 16 Jun 2020 07:59:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:26: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:59:26: #2 alternative fragment length(s) may be 4,124 bps INFO @ Tue, 16 Jun 2020 07:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10_model.r INFO @ Tue, 16 Jun 2020 07:59:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:26: #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 @ Tue, 16 Jun 2020 07:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:59:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:40: 1000000 INFO @ Tue, 16 Jun 2020 07:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:46: 2000000 INFO @ Tue, 16 Jun 2020 07:59:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:59:57: 4000000 INFO @ Tue, 16 Jun 2020 07:59:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:59:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:59:58: #1 total tags in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:59:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:59:58: #1 tags after filtering in treatment: 4124837 INFO @ Tue, 16 Jun 2020 07:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:58: #2 number of paired peaks: 1543 INFO @ Tue, 16 Jun 2020 07:59:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:59: #2 predicted fragment length is 124 bps INFO @ Tue, 16 Jun 2020 07:59:59: #2 alternative fragment length(s) may be 4,124 bps INFO @ Tue, 16 Jun 2020 07:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20_model.r INFO @ Tue, 16 Jun 2020 07:59:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:00:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144183/SRX2144183.20_summits.bed INFO @ Tue, 16 Jun 2020 08:00:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (245 records, 4 fields): 1 millis CompletedMACS2peakCalling