Job ID = 6367966 SRX = SRX4456925 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:17 prefetch.2.10.7: 1) Downloading 'SRR7591866'... 2020-06-15T23:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:03 prefetch.2.10.7: 'SRR7591866' is valid 2020-06-15T23:42:03 prefetch.2.10.7: 1) 'SRR7591866' was downloaded successfully Read 3399971 spots for SRR7591866/SRR7591866.sra Written 3399971 spots for SRR7591866/SRR7591866.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: 00:00:45 3399971 reads; of these: 3399971 (100.00%) were unpaired; of these: 290390 (8.54%) aligned 0 times 2682197 (78.89%) aligned exactly 1 time 427384 (12.57%) aligned >1 times 91.46% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 324637 / 3109581 = 0.1044 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 08:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.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 08:44:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:08: 1000000 INFO @ Tue, 16 Jun 2020 08:44:14: 2000000 INFO @ Tue, 16 Jun 2020 08:44:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:44:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:44:18: #1 total tags in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:44:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:18: #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 08:44:18: #1 tags after filtering in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:18: #2 number of paired peaks: 1818 INFO @ Tue, 16 Jun 2020 08:44:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:18: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:44:18: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:44:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05_model.r INFO @ Tue, 16 Jun 2020 08:44:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1528 records, 4 fields): 2 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 08:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.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 08:44:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:39: 1000000 INFO @ Tue, 16 Jun 2020 08:44:46: 2000000 INFO @ Tue, 16 Jun 2020 08:44:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:44:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:44:52: #1 total tags in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:44:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:52: #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 08:44:52: #1 tags after filtering in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:52: #2 number of paired peaks: 1818 INFO @ Tue, 16 Jun 2020 08:44:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:52: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:44:52: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10_model.r INFO @ Tue, 16 Jun 2020 08:44:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:58: #3 Call peaks for each chromosome... 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 08:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.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 08:45:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:15: 2000000 INFO @ Tue, 16 Jun 2020 08:45:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:19: #1 total tags in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:45:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:19: #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 08:45:19: #1 tags after filtering in treatment: 2784944 INFO @ Tue, 16 Jun 2020 08:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:19: #2 number of paired peaks: 1818 INFO @ Tue, 16 Jun 2020 08:45:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:19: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:45:19: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20_model.r INFO @ Tue, 16 Jun 2020 08:45:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456925/SRX4456925.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (161 records, 4 fields): 1 millis CompletedMACS2peakCalling