Job ID = 6366337 SRX = SRX113611 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:44 prefetch.2.10.7: 1) Downloading 'SRR393711'... 2020-06-15T22:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:44 prefetch.2.10.7: 'SRR393711' is valid 2020-06-15T22:55:44 prefetch.2.10.7: 1) 'SRR393711' was downloaded successfully Read 15876751 spots for SRR393711/SRR393711.sra Written 15876751 spots for SRR393711/SRR393711.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: 00:03:39 15876751 reads; of these: 15876751 (100.00%) were unpaired; of these: 901644 (5.68%) aligned 0 times 9945136 (62.64%) aligned exactly 1 time 5029971 (31.68%) aligned >1 times 94.32% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 7771614 / 14975107 = 0.5190 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 08:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.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 08:03:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:27: 1000000 INFO @ Tue, 16 Jun 2020 08:03:32: 2000000 INFO @ Tue, 16 Jun 2020 08:03:37: 3000000 INFO @ Tue, 16 Jun 2020 08:03:42: 4000000 INFO @ Tue, 16 Jun 2020 08:03:46: 5000000 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 08:03:51: 6000000 INFO @ Tue, 16 Jun 2020 08:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.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 08:03:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:56: 7000000 INFO @ Tue, 16 Jun 2020 08:03:57: 1000000 INFO @ Tue, 16 Jun 2020 08:03:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:03:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:03:57: #1 total tags in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:03:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:57: #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 08:03:57: #1 tags after filtering in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:03:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:58: #2 number of paired peaks: 5700 INFO @ Tue, 16 Jun 2020 08:03:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:59: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:03:59: #2 alternative fragment length(s) may be 1,157,179 bps INFO @ Tue, 16 Jun 2020 08:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05_model.r INFO @ Tue, 16 Jun 2020 08:03:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:02: 2000000 INFO @ Tue, 16 Jun 2020 08:04:07: 3000000 INFO @ Tue, 16 Jun 2020 08:04:12: 4000000 INFO @ Tue, 16 Jun 2020 08:04:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:17: 5000000 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 08:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.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 08:04:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:22: 6000000 INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3274 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:26: 1000000 INFO @ Tue, 16 Jun 2020 08:04:27: 7000000 INFO @ Tue, 16 Jun 2020 08:04:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:04:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:04:28: #1 total tags in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:04:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:28: #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 08:04:28: #1 tags after filtering in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:29: #2 number of paired peaks: 5700 INFO @ Tue, 16 Jun 2020 08:04:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:29: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:04:29: #2 alternative fragment length(s) may be 1,157,179 bps INFO @ Tue, 16 Jun 2020 08:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10_model.r INFO @ Tue, 16 Jun 2020 08:04:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:31: 2000000 INFO @ Tue, 16 Jun 2020 08:04:36: 3000000 INFO @ Tue, 16 Jun 2020 08:04:40: 4000000 INFO @ Tue, 16 Jun 2020 08:04:45: 5000000 INFO @ Tue, 16 Jun 2020 08:04:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:49: 6000000 INFO @ Tue, 16 Jun 2020 08:04:54: 7000000 INFO @ Tue, 16 Jun 2020 08:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:04:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:04:55: #1 total tags in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:04:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:55: #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 08:04:55: #1 tags after filtering in treatment: 7203493 INFO @ Tue, 16 Jun 2020 08:04:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:56: #2 number of paired peaks: 5700 INFO @ Tue, 16 Jun 2020 08:04:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:56: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:04:56: #2 alternative fragment length(s) may be 1,157,179 bps INFO @ Tue, 16 Jun 2020 08:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20_model.r INFO @ Tue, 16 Jun 2020 08:04:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113611/SRX113611.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 1 millis CompletedMACS2peakCalling