Job ID = 6366623 SRX = SRX2144170 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:52:11 prefetch.2.10.7: 1) Downloading 'SRR4188774'... 2020-06-15T22:52:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:48 prefetch.2.10.7: 'SRR4188774' is valid 2020-06-15T22:52:48 prefetch.2.10.7: 1) 'SRR4188774' was downloaded successfully Read 5531968 spots for SRR4188774/SRR4188774.sra Written 5531968 spots for SRR4188774/SRR4188774.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: 00:01:03 5531968 reads; of these: 5531968 (100.00%) were unpaired; of these: 1028895 (18.60%) aligned 0 times 3905688 (70.60%) aligned exactly 1 time 597385 (10.80%) aligned >1 times 81.40% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 335939 / 4503073 = 0.0746 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 07:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.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 07:55:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:45: 1000000 INFO @ Tue, 16 Jun 2020 07:55:51: 2000000 INFO @ Tue, 16 Jun 2020 07:55:57: 3000000 INFO @ Tue, 16 Jun 2020 07:56:02: 4000000 INFO @ Tue, 16 Jun 2020 07:56:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:03: #1 total tags in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:56:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:03: #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 07:56:03: #1 tags after filtering in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:03: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:04: #2 number of paired peaks: 3271 INFO @ Tue, 16 Jun 2020 07:56:04: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:04: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:04: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:04: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:04: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:56:04: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05_model.r INFO @ Tue, 16 Jun 2020 07:56:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:04: #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 07:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.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 07:56:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:15: 1000000 INFO @ Tue, 16 Jun 2020 07:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.05_summits.bed INFO @ Tue, 16 Jun 2020 07:56:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3040 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:56:21: 2000000 INFO @ Tue, 16 Jun 2020 07:56:27: 3000000 INFO @ Tue, 16 Jun 2020 07:56:33: 4000000 INFO @ Tue, 16 Jun 2020 07:56:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:34: #1 total tags in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:56:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:34: #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 07:56:34: #1 tags after filtering in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:35: #2 number of paired peaks: 3271 INFO @ Tue, 16 Jun 2020 07:56:35: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:35: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:56:35: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10_model.r INFO @ Tue, 16 Jun 2020 07:56:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:35: #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 07:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.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 07:56:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:45: 1000000 INFO @ Tue, 16 Jun 2020 07:56:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:51: 2000000 INFO @ Tue, 16 Jun 2020 07:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.10_summits.bed INFO @ Tue, 16 Jun 2020 07:56:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1516 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:56:57: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:03: 4000000 INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:57:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:57:04: #1 total tags in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:57:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:04: #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 07:57:04: #1 tags after filtering in treatment: 4167134 INFO @ Tue, 16 Jun 2020 07:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:04: #2 number of paired peaks: 3271 INFO @ Tue, 16 Jun 2020 07:57:04: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:05: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:57:05: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20_model.r INFO @ Tue, 16 Jun 2020 07:57:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:57:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144170/SRX2144170.20_summits.bed INFO @ Tue, 16 Jun 2020 07:57:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis CompletedMACS2peakCalling