Job ID = 6366956 SRX = SRX2576656 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:31 prefetch.2.10.7: 1) Downloading 'SRR5272613'... 2020-06-15T23:10:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:14 prefetch.2.10.7: 1) 'SRR5272613' was downloaded successfully Read 25014594 spots for SRR5272613/SRR5272613.sra Written 25014594 spots for SRR5272613/SRR5272613.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: 00:05:10 25014594 reads; of these: 25014594 (100.00%) were unpaired; of these: 3059136 (12.23%) aligned 0 times 18279616 (73.08%) aligned exactly 1 time 3675842 (14.69%) aligned >1 times 87.77% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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 12 files... [bam_rmdupse_core] 12573840 / 21955458 = 0.5727 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 08:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.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 08:24:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:19: 1000000 INFO @ Tue, 16 Jun 2020 08:24:24: 2000000 INFO @ Tue, 16 Jun 2020 08:24:28: 3000000 INFO @ Tue, 16 Jun 2020 08:24:33: 4000000 INFO @ Tue, 16 Jun 2020 08:24:38: 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 08:24:44: 6000000 INFO @ Tue, 16 Jun 2020 08:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.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 08:24:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:49: 7000000 INFO @ Tue, 16 Jun 2020 08:24:49: 1000000 INFO @ Tue, 16 Jun 2020 08:24:54: 8000000 INFO @ Tue, 16 Jun 2020 08:24:55: 2000000 INFO @ Tue, 16 Jun 2020 08:24:59: 9000000 INFO @ Tue, 16 Jun 2020 08:25:00: 3000000 INFO @ Tue, 16 Jun 2020 08:25:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:25:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:25:01: #1 total tags in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:25:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:01: #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 08:25:01: #1 tags after filtering in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:02: #2 number of paired peaks: 1341 INFO @ Tue, 16 Jun 2020 08:25:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:02: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:25:02: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05_model.r INFO @ Tue, 16 Jun 2020 08:25:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:05: 4000000 INFO @ Tue, 16 Jun 2020 08:25:10: 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 08:25:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.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 08:25:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:15: 6000000 INFO @ Tue, 16 Jun 2020 08:25:19: 1000000 INFO @ Tue, 16 Jun 2020 08:25:20: 7000000 INFO @ Tue, 16 Jun 2020 08:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:24: 2000000 INFO @ Tue, 16 Jun 2020 08:25:25: 8000000 INFO @ Tue, 16 Jun 2020 08:25:29: 3000000 INFO @ Tue, 16 Jun 2020 08:25:30: 9000000 INFO @ Tue, 16 Jun 2020 08:25:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:25:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:25:31: #1 total tags in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:25:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:31: #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 08:25:32: #1 tags after filtering in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:32: #2 number of paired peaks: 1341 INFO @ Tue, 16 Jun 2020 08:25:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:32: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:25:32: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10_model.r INFO @ Tue, 16 Jun 2020 08:25:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3762 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:34: 4000000 INFO @ Tue, 16 Jun 2020 08:25:39: 5000000 INFO @ Tue, 16 Jun 2020 08:25:43: 6000000 INFO @ Tue, 16 Jun 2020 08:25:48: 7000000 INFO @ Tue, 16 Jun 2020 08:25:53: 8000000 INFO @ Tue, 16 Jun 2020 08:25:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:58: 9000000 INFO @ Tue, 16 Jun 2020 08:26:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:26:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:26:00: #1 total tags in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:26:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:00: #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 08:26:00: #1 tags after filtering in treatment: 9381618 INFO @ Tue, 16 Jun 2020 08:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:01: #2 number of paired peaks: 1341 INFO @ Tue, 16 Jun 2020 08:26:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:01: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:26:01: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20_model.r INFO @ Tue, 16 Jun 2020 08:26:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2858 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576656/SRX2576656.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1995 records, 4 fields): 3 millis CompletedMACS2peakCalling