Job ID = 6366001 SRX = SRX044012 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:53 prefetch.2.10.7: 1) Downloading 'SRR107594'... 2020-06-15T23:00:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:16 prefetch.2.10.7: 'SRR107594' is valid 2020-06-15T23:01:16 prefetch.2.10.7: 1) 'SRR107594' was downloaded successfully Read 3021900 spots for SRR107594/SRR107594.sra Written 3021900 spots for SRR107594/SRR107594.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: 00:00:21 3021900 reads; of these: 3021900 (100.00%) were unpaired; of these: 1066292 (35.29%) aligned 0 times 1688104 (55.86%) aligned exactly 1 time 267504 (8.85%) aligned >1 times 64.71% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 357252 / 1955608 = 0.1827 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 08:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.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 08:02:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:51: 1000000 INFO @ Tue, 16 Jun 2020 08:02:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:02:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:02:54: #1 total tags in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:02:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:54: #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 08:02:54: #1 tags after filtering in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:54: #2 number of paired peaks: 1633 INFO @ Tue, 16 Jun 2020 08:02:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:54: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:02:54: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05_model.r INFO @ Tue, 16 Jun 2020 08:02:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2733 records, 4 fields): 9 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 08:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.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 08:03:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:20: 1000000 INFO @ Tue, 16 Jun 2020 08:03:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:23: #1 total tags in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:03:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:23: #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 08:03:23: #1 tags after filtering in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:23: #2 number of paired peaks: 1633 INFO @ Tue, 16 Jun 2020 08:03:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:23: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:03:23: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10_model.r INFO @ Tue, 16 Jun 2020 08:03:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1386 records, 4 fields): 3 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 08:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.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 08:03:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:53: #1 total tags in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:03:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:53: #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 08:03:53: #1 tags after filtering in treatment: 1598356 INFO @ Tue, 16 Jun 2020 08:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:53: #2 number of paired peaks: 1633 INFO @ Tue, 16 Jun 2020 08:03:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:53: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:03:53: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20_model.r INFO @ Tue, 16 Jun 2020 08:03:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044012/SRX044012.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling