Job ID = 6367686 SRX = SRX3923759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:05 prefetch.2.10.7: 1) Downloading 'SRR6983681'... 2020-06-15T23:32:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:43 prefetch.2.10.7: 1) 'SRR6983681' was downloaded successfully 2020-06-15T23:38:43 prefetch.2.10.7: 'SRR6983681' has 0 unresolved dependencies Read 64808971 spots for SRR6983681/SRR6983681.sra Written 64808971 spots for SRR6983681/SRR6983681.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: 00:14:26 64808971 reads; of these: 64808971 (100.00%) were unpaired; of these: 2926629 (4.52%) aligned 0 times 52579126 (81.13%) aligned exactly 1 time 9303216 (14.35%) aligned >1 times 95.48% overall alignment rate Time searching: 00:14:26 Overall time: 00:14:26 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_sort_core] merging from 28 files... [bam_rmdupse_core] 53357553 / 61882342 = 0.8622 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 09:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.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 09:04:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:02: 1000000 INFO @ Tue, 16 Jun 2020 09:05:10: 2000000 INFO @ Tue, 16 Jun 2020 09:05:17: 3000000 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 09:05:24: 4000000 INFO @ Tue, 16 Jun 2020 09:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.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 09:05:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:31: 5000000 INFO @ Tue, 16 Jun 2020 09:05:33: 1000000 INFO @ Tue, 16 Jun 2020 09:05:39: 6000000 INFO @ Tue, 16 Jun 2020 09:05:40: 2000000 INFO @ Tue, 16 Jun 2020 09:05:46: 7000000 INFO @ Tue, 16 Jun 2020 09:05:48: 3000000 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 09:05:53: 8000000 INFO @ Tue, 16 Jun 2020 09:05:55: 4000000 INFO @ Tue, 16 Jun 2020 09:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.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 09:05:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:05:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:05:57: #1 total tags in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:05:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:57: #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 09:05:57: #1 tags after filtering in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:58: #2 number of paired peaks: 1739 INFO @ Tue, 16 Jun 2020 09:05:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:58: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:05:58: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 09:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05_model.r INFO @ Tue, 16 Jun 2020 09:05:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:02: 5000000 INFO @ Tue, 16 Jun 2020 09:06:02: 1000000 INFO @ Tue, 16 Jun 2020 09:06:10: 2000000 INFO @ Tue, 16 Jun 2020 09:06:10: 6000000 INFO @ Tue, 16 Jun 2020 09:06:17: 3000000 INFO @ Tue, 16 Jun 2020 09:06:17: 7000000 INFO @ Tue, 16 Jun 2020 09:06:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:24: 4000000 INFO @ Tue, 16 Jun 2020 09:06:24: 8000000 INFO @ Tue, 16 Jun 2020 09:06:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:28: #1 total tags in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:06:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:28: #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 09:06:28: #1 tags after filtering in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:29: #2 number of paired peaks: 1739 INFO @ Tue, 16 Jun 2020 09:06:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:29: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:06:29: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 09:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10_model.r INFO @ Tue, 16 Jun 2020 09:06:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:31: 5000000 INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7861 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:06:45: 7000000 INFO @ Tue, 16 Jun 2020 09:06:51: 8000000 INFO @ Tue, 16 Jun 2020 09:06:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:55: #1 total tags in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:06:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:55: #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 09:06:55: #1 tags after filtering in treatment: 8524789 INFO @ Tue, 16 Jun 2020 09:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:56: #2 number of paired peaks: 1739 INFO @ Tue, 16 Jun 2020 09:06:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:56: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:06:56: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 09:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20_model.r INFO @ Tue, 16 Jun 2020 09:06:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5479 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3923759/SRX3923759.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3196 records, 4 fields): 4 millis CompletedMACS2peakCalling