Job ID = 6366727 SRX = SRX2228880 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:38 prefetch.2.10.7: 1) Downloading 'SRR4380336'... 2020-06-15T23:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:43 prefetch.2.10.7: 'SRR4380336' is valid 2020-06-15T23:03:43 prefetch.2.10.7: 1) 'SRR4380336' was downloaded successfully 2020-06-15T23:03:43 prefetch.2.10.7: 'SRR4380336' has 0 unresolved dependencies Read 18386343 spots for SRR4380336/SRR4380336.sra Written 18386343 spots for SRR4380336/SRR4380336.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: 00:02:29 18386343 reads; of these: 18386343 (100.00%) were unpaired; of these: 11695378 (63.61%) aligned 0 times 5665713 (30.81%) aligned exactly 1 time 1025252 (5.58%) aligned >1 times 36.39% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 1177287 / 6690965 = 0.1760 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 08:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.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 08:09:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:24: 1000000 INFO @ Tue, 16 Jun 2020 08:09:30: 2000000 INFO @ Tue, 16 Jun 2020 08:09:35: 3000000 INFO @ Tue, 16 Jun 2020 08:09:41: 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 @ Tue, 16 Jun 2020 08:09:47: 5000000 INFO @ Tue, 16 Jun 2020 08:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.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 08:09:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:09:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:09:50: #1 total tags in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:09:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:50: #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 08:09:50: #1 tags after filtering in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:50: #2 number of paired peaks: 1138 INFO @ Tue, 16 Jun 2020 08:09:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:50: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 08:09:50: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 08:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05_model.r INFO @ Tue, 16 Jun 2020 08:09:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:54: 1000000 INFO @ Tue, 16 Jun 2020 08:10:00: 2000000 INFO @ Tue, 16 Jun 2020 08:10:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:06: 3000000 INFO @ Tue, 16 Jun 2020 08:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2323 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:12: 4000000 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 08:10:18: 5000000 INFO @ Tue, 16 Jun 2020 08:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.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 08:10:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:10:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:10:22: #1 total tags in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:10:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:22: #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 08:10:22: #1 tags after filtering in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:22: #2 number of paired peaks: 1138 INFO @ Tue, 16 Jun 2020 08:10:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:22: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 08:10:22: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 08:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10_model.r INFO @ Tue, 16 Jun 2020 08:10:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:26: 1000000 INFO @ Tue, 16 Jun 2020 08:10:33: 2000000 INFO @ Tue, 16 Jun 2020 08:10:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:40: 3000000 INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1432 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:47: 4000000 INFO @ Tue, 16 Jun 2020 08:10:54: 5000000 INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:10:58: #1 total tags in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:10:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:58: #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 08:10:58: #1 tags after filtering in treatment: 5513678 INFO @ Tue, 16 Jun 2020 08:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:58: #2 number of paired peaks: 1138 INFO @ Tue, 16 Jun 2020 08:10:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:58: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 08:10:58: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 08:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20_model.r INFO @ Tue, 16 Jun 2020 08:10:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228880/SRX2228880.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 2 millis CompletedMACS2peakCalling