Job ID = 6367699 SRX = SRX395523 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR1054245'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:03 prefetch.2.10.7: 'SRR1054245' is valid 2020-06-15T23:33:03 prefetch.2.10.7: 1) 'SRR1054245' was downloaded successfully Read 3477938 spots for SRR1054245/SRR1054245.sra Written 3477938 spots for SRR1054245/SRR1054245.sra 2020-06-15T23:33:24 prefetch.2.10.7: 1) Downloading 'SRR1054246'... 2020-06-15T23:33:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:53 prefetch.2.10.7: 'SRR1054246' is valid 2020-06-15T23:33:53 prefetch.2.10.7: 1) 'SRR1054246' was downloaded successfully Read 1015557 spots for SRR1054246/SRR1054246.sra Written 1015557 spots for SRR1054246/SRR1054246.sra 2020-06-15T23:34:07 prefetch.2.10.7: 1) Downloading 'SRR1054247'... 2020-06-15T23:34:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:31 prefetch.2.10.7: 'SRR1054247' is valid 2020-06-15T23:34:31 prefetch.2.10.7: 1) 'SRR1054247' was downloaded successfully Read 1540309 spots for SRR1054247/SRR1054247.sra Written 1540309 spots for SRR1054247/SRR1054247.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: 00:00:41 6033804 reads; of these: 6033804 (100.00%) were unpaired; of these: 2831421 (46.93%) aligned 0 times 2515242 (41.69%) aligned exactly 1 time 687141 (11.39%) aligned >1 times 53.07% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 716348 / 3202383 = 0.2237 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 08:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.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 08:36:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:27: 1000000 INFO @ Tue, 16 Jun 2020 08:36:32: 2000000 INFO @ Tue, 16 Jun 2020 08:36:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:35: #1 total tags in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:36:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:35: #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 08:36:35: #1 tags after filtering in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:35: #2 number of paired peaks: 1814 INFO @ Tue, 16 Jun 2020 08:36:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:35: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:36:35: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05_model.r INFO @ Tue, 16 Jun 2020 08:36:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2306 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.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 08:36:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:58: 1000000 INFO @ Tue, 16 Jun 2020 08:37:04: 2000000 INFO @ Tue, 16 Jun 2020 08:37:07: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:07: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:07: #1 total tags in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:37:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:07: #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 08:37:07: #1 tags after filtering in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:07: #2 number of paired peaks: 1814 INFO @ Tue, 16 Jun 2020 08:37:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:08: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:37:08: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10_model.r INFO @ Tue, 16 Jun 2020 08:37:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1132 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.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 08:37:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:27: 1000000 INFO @ Tue, 16 Jun 2020 08:37:32: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:37:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:37:35: #1 total tags in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:37:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:35: #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 08:37:35: #1 tags after filtering in treatment: 2486035 INFO @ Tue, 16 Jun 2020 08:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:35: #2 number of paired peaks: 1814 INFO @ Tue, 16 Jun 2020 08:37:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:35: #2 predicted fragment length is 179 bps INFO @ Tue, 16 Jun 2020 08:37:35: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 16 Jun 2020 08:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20_model.r INFO @ Tue, 16 Jun 2020 08:37:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395523/SRX395523.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 1 millis CompletedMACS2peakCalling