Job ID = 6367973 SRX = SRX4456932 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:32 prefetch.2.10.7: 1) Downloading 'SRR7591873'... 2020-06-15T23:47:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:24 prefetch.2.10.7: 'SRR7591873' is valid 2020-06-15T23:49:24 prefetch.2.10.7: 1) 'SRR7591873' was downloaded successfully Read 11930630 spots for SRR7591873/SRR7591873.sra Written 11930630 spots for SRR7591873/SRR7591873.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: 00:02:26 11930630 reads; of these: 11930630 (100.00%) were unpaired; of these: 2215884 (18.57%) aligned 0 times 7120105 (59.68%) aligned exactly 1 time 2594641 (21.75%) aligned >1 times 81.43% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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_rmdupse_core] 1472457 / 9714746 = 0.1516 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 08:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.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 08:55:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:19: 1000000 INFO @ Tue, 16 Jun 2020 08:55:24: 2000000 INFO @ Tue, 16 Jun 2020 08:55:29: 3000000 INFO @ Tue, 16 Jun 2020 08:55:34: 4000000 INFO @ Tue, 16 Jun 2020 08:55:39: 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 08:55:44: 6000000 INFO @ Tue, 16 Jun 2020 08:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.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 08:55:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:49: 7000000 INFO @ Tue, 16 Jun 2020 08:55:49: 1000000 INFO @ Tue, 16 Jun 2020 08:55:54: 8000000 INFO @ Tue, 16 Jun 2020 08:55:55: 2000000 INFO @ Tue, 16 Jun 2020 08:55:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:56: #1 total tags in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:55:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:56: #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 08:55:56: #1 tags after filtering in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:55:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:57: #2 number of paired peaks: 1459 INFO @ Tue, 16 Jun 2020 08:55:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:57: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 08:55:57: #2 alternative fragment length(s) may be 3,130 bps INFO @ Tue, 16 Jun 2020 08:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05_model.r INFO @ Tue, 16 Jun 2020 08:55:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:00: 3000000 INFO @ Tue, 16 Jun 2020 08:56:05: 4000000 INFO @ Tue, 16 Jun 2020 08:56:10: 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 08:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.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 08:56:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:15: 6000000 INFO @ Tue, 16 Jun 2020 08:56:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:20: 7000000 INFO @ Tue, 16 Jun 2020 08:56:20: 1000000 INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1514 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:26: 8000000 INFO @ Tue, 16 Jun 2020 08:56:27: 2000000 INFO @ Tue, 16 Jun 2020 08:56:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:27: #1 total tags in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:56:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:27: #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 08:56:27: #1 tags after filtering in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:28: #2 number of paired peaks: 1459 INFO @ Tue, 16 Jun 2020 08:56:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:28: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 08:56:28: #2 alternative fragment length(s) may be 3,130 bps INFO @ Tue, 16 Jun 2020 08:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10_model.r INFO @ Tue, 16 Jun 2020 08:56:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:33: 3000000 INFO @ Tue, 16 Jun 2020 08:56:39: 4000000 INFO @ Tue, 16 Jun 2020 08:56:45: 5000000 INFO @ Tue, 16 Jun 2020 08:56:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:51: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:58: 7000000 INFO @ Tue, 16 Jun 2020 08:57:04: 8000000 INFO @ Tue, 16 Jun 2020 08:57:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:05: #1 total tags in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:57:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:05: #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 08:57:05: #1 tags after filtering in treatment: 8242289 INFO @ Tue, 16 Jun 2020 08:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:06: #2 number of paired peaks: 1459 INFO @ Tue, 16 Jun 2020 08:57:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:06: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 08:57:06: #2 alternative fragment length(s) may be 3,130 bps INFO @ Tue, 16 Jun 2020 08:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20_model.r INFO @ Tue, 16 Jun 2020 08:57:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456932/SRX4456932.20_summits.bed INFO @ Tue, 16 Jun 2020 08:57:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling