Job ID = 6368193 SRX = SRX494877 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:01 prefetch.2.10.7: 1) Downloading 'SRR1198409'... 2020-06-16T00:06:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:24 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:24 prefetch.2.10.7: 1) 'SRR1198409' was downloaded successfully Read 17837914 spots for SRR1198409/SRR1198409.sra Written 17837914 spots for SRR1198409/SRR1198409.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: 00:04:01 17837914 reads; of these: 17837914 (100.00%) were unpaired; of these: 4112404 (23.05%) aligned 0 times 10808412 (60.59%) aligned exactly 1 time 2917098 (16.35%) aligned >1 times 76.95% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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 8 files... [bam_rmdupse_core] 7761376 / 13725510 = 0.5655 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 09:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.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 09:15:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:32: 1000000 INFO @ Tue, 16 Jun 2020 09:15:39: 2000000 INFO @ Tue, 16 Jun 2020 09:15:45: 3000000 INFO @ Tue, 16 Jun 2020 09:15:52: 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 09:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.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 09:15:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:58: 5000000 INFO @ Tue, 16 Jun 2020 09:16:03: 1000000 INFO @ Tue, 16 Jun 2020 09:16:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:05: #1 total tags in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:16:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:05: #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 09:16:05: #1 tags after filtering in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:16:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:06: #2 number of paired peaks: 2308 INFO @ Tue, 16 Jun 2020 09:16:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:06: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:16:06: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:16:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05_model.r INFO @ Tue, 16 Jun 2020 09:16:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:10: 2000000 INFO @ Tue, 16 Jun 2020 09:16:16: 3000000 INFO @ Tue, 16 Jun 2020 09:16:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:22: 4000000 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 09:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.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 09:16:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:29: 5000000 INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4715 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:32: 1000000 INFO @ Tue, 16 Jun 2020 09:16:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:36: #1 total tags in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:16:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:36: #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 09:16:36: #1 tags after filtering in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:36: #2 number of paired peaks: 2308 INFO @ Tue, 16 Jun 2020 09:16:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:37: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:16:37: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10_model.r INFO @ Tue, 16 Jun 2020 09:16:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:38: 2000000 INFO @ Tue, 16 Jun 2020 09:16:44: 3000000 INFO @ Tue, 16 Jun 2020 09:16:50: 4000000 INFO @ Tue, 16 Jun 2020 09:16:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:55: 5000000 INFO @ Tue, 16 Jun 2020 09:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:01: Done! INFO @ Tue, 16 Jun 2020 09:17:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:17:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:17:01: #1 total tags in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:17:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3282 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:01: #1 tags after filtering in treatment: 5964134 INFO @ Tue, 16 Jun 2020 09:17:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:01: #2 number of paired peaks: 2308 INFO @ Tue, 16 Jun 2020 09:17:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:02: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:17:02: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20_model.r INFO @ Tue, 16 Jun 2020 09:17:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494877/SRX494877.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2150 records, 4 fields): 4 millis CompletedMACS2peakCalling