Job ID = 6365871 SRX = SRX005628 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:29 prefetch.2.10.7: 1) Downloading 'SRR017597'... 2020-06-15T22:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:05 prefetch.2.10.7: 'SRR017597' is valid 2020-06-15T22:28:05 prefetch.2.10.7: 1) 'SRR017597' was downloaded successfully Read 7403385 spots for SRR017597/SRR017597.sra Written 7403385 spots for SRR017597/SRR017597.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: 00:01:01 7403385 reads; of these: 7403385 (100.00%) were unpaired; of these: 2027279 (27.38%) aligned 0 times 4587810 (61.97%) aligned exactly 1 time 788296 (10.65%) aligned >1 times 72.62% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 1549055 / 5376106 = 0.2881 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 07:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.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 07:31:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:10: 1000000 INFO @ Tue, 16 Jun 2020 07:31:16: 2000000 INFO @ Tue, 16 Jun 2020 07:31:23: 3000000 INFO @ Tue, 16 Jun 2020 07:31:28: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:31:28: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:31:28: #1 total tags in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:31:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:28: #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 07:31:28: #1 tags after filtering in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:29: #2 number of paired peaks: 1939 INFO @ Tue, 16 Jun 2020 07:31:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:29: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:31:29: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 07:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05_model.r INFO @ Tue, 16 Jun 2020 07:31:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:29: #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 07:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.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 07:31:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:40: 1000000 INFO @ Tue, 16 Jun 2020 07:31:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:46: 2000000 INFO @ Tue, 16 Jun 2020 07:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.05_summits.bed INFO @ Tue, 16 Jun 2020 07:31:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2978 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:31:52: 3000000 INFO @ Tue, 16 Jun 2020 07:31:57: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:31:57: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:31:57: #1 total tags in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:31:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:57: #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 07:31:57: #1 tags after filtering in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:58: #2 number of paired peaks: 1939 INFO @ Tue, 16 Jun 2020 07:31:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:58: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:31:58: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 07:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10_model.r INFO @ Tue, 16 Jun 2020 07:31:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:58: #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 07:32:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.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 07:32:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:10: 1000000 INFO @ Tue, 16 Jun 2020 07:32:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.10_summits.bed INFO @ Tue, 16 Jun 2020 07:32:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1257 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:32:17: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:32:23: 3000000 INFO @ Tue, 16 Jun 2020 07:32:28: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:32:28: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:32:28: #1 total tags in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:32:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:28: #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 07:32:28: #1 tags after filtering in treatment: 3827051 INFO @ Tue, 16 Jun 2020 07:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:29: #2 number of paired peaks: 1939 INFO @ Tue, 16 Jun 2020 07:32:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:29: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:32:29: #2 alternative fragment length(s) may be 4,127 bps INFO @ Tue, 16 Jun 2020 07:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20_model.r INFO @ Tue, 16 Jun 2020 07:32:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:32:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005628/SRX005628.20_summits.bed INFO @ Tue, 16 Jun 2020 07:32:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling