Job ID = 6367216 SRX = SRX3043402 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:46 prefetch.2.10.7: 1) Downloading 'SRR5875886'... 2020-06-15T23:18:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:19:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:19:39 prefetch.2.10.7: 'SRR5875886' is valid 2020-06-15T23:19:39 prefetch.2.10.7: 1) 'SRR5875886' was downloaded successfully Read 7667127 spots for SRR5875886/SRR5875886.sra Written 7667127 spots for SRR5875886/SRR5875886.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: 00:02:08 7667127 reads; of these: 7667127 (100.00%) were unpaired; of these: 225253 (2.94%) aligned 0 times 6604227 (86.14%) aligned exactly 1 time 837647 (10.93%) aligned >1 times 97.06% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 662324 / 7441874 = 0.0890 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 08:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.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 08:24:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:55: 1000000 INFO @ Tue, 16 Jun 2020 08:25:02: 2000000 INFO @ Tue, 16 Jun 2020 08:25:09: 3000000 INFO @ Tue, 16 Jun 2020 08:25:16: 4000000 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 08:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.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 08:25:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:23: 5000000 INFO @ Tue, 16 Jun 2020 08:25:26: 1000000 INFO @ Tue, 16 Jun 2020 08:25:31: 6000000 INFO @ Tue, 16 Jun 2020 08:25:34: 2000000 INFO @ Tue, 16 Jun 2020 08:25:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:36: #1 total tags in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:25:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:36: #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 08:25:36: #1 tags after filtering in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:37: #2 number of paired peaks: 1194 INFO @ Tue, 16 Jun 2020 08:25:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:37: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05_model.r INFO @ Tue, 16 Jun 2020 08:25:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:41: 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 08:25:48: 4000000 INFO @ Tue, 16 Jun 2020 08:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.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 08:25:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:55: 5000000 INFO @ Tue, 16 Jun 2020 08:25:56: 1000000 INFO @ Tue, 16 Jun 2020 08:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4294 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:03: 6000000 INFO @ Tue, 16 Jun 2020 08:26:04: 2000000 INFO @ Tue, 16 Jun 2020 08:26:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:09: #1 total tags in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:26:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:09: #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 08:26:09: #1 tags after filtering in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:26:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:09: #2 number of paired peaks: 1194 INFO @ Tue, 16 Jun 2020 08:26:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:09: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:26:09: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10_model.r INFO @ Tue, 16 Jun 2020 08:26:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:11: 3000000 INFO @ Tue, 16 Jun 2020 08:26:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:26: 5000000 INFO @ Tue, 16 Jun 2020 08:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2971 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:33: 6000000 INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:39: #1 total tags in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:26:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:39: #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 08:26:39: #1 tags after filtering in treatment: 6779550 INFO @ Tue, 16 Jun 2020 08:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:39: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:39: #2 number of paired peaks: 1194 INFO @ Tue, 16 Jun 2020 08:26:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:40: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 08:26:40: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 16 Jun 2020 08:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20_model.r INFO @ Tue, 16 Jun 2020 08:26:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043402/SRX3043402.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1675 records, 4 fields): 3 millis CompletedMACS2peakCalling