Job ID = 6367326 SRX = SRX331088 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:46 prefetch.2.10.7: 1) Downloading 'SRR947317'... 2020-06-15T23:16:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:08 prefetch.2.10.7: 'SRR947317' is valid 2020-06-15T23:17:08 prefetch.2.10.7: 1) 'SRR947317' was downloaded successfully Read 4800550 spots for SRR947317/SRR947317.sra Written 4800550 spots for SRR947317/SRR947317.sra 2020-06-15T23:17:31 prefetch.2.10.7: 1) Downloading 'SRR947318'... 2020-06-15T23:17:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:57 prefetch.2.10.7: 'SRR947318' is valid 2020-06-15T23:17:57 prefetch.2.10.7: 1) 'SRR947318' was downloaded successfully Read 5992012 spots for SRR947318/SRR947318.sra Written 5992012 spots for SRR947318/SRR947318.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:08 10792562 reads; of these: 10792562 (100.00%) were unpaired; of these: 6178649 (57.25%) aligned 0 times 3984953 (36.92%) aligned exactly 1 time 628960 (5.83%) aligned >1 times 42.75% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 1585630 / 4613913 = 0.3437 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 08:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.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 08:20:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:43: 1000000 INFO @ Tue, 16 Jun 2020 08:20:49: 2000000 INFO @ Tue, 16 Jun 2020 08:20:54: 3000000 INFO @ Tue, 16 Jun 2020 08:20:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:20:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:20:54: #1 total tags in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:20:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:54: #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 08:20:54: #1 tags after filtering in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:55: #2 number of paired peaks: 2179 INFO @ Tue, 16 Jun 2020 08:20:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:55: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:20:55: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05_model.r INFO @ Tue, 16 Jun 2020 08:20:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4547 records, 4 fields): 5 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 08:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.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 08:21:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:13: 1000000 INFO @ Tue, 16 Jun 2020 08:21:19: 2000000 INFO @ Tue, 16 Jun 2020 08:21:25: 3000000 INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:25: #1 total tags in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:21:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:25: #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 08:21:25: #1 tags after filtering in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:25: #2 number of paired peaks: 2179 INFO @ Tue, 16 Jun 2020 08:21:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:25: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:21:25: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10_model.r INFO @ Tue, 16 Jun 2020 08:21:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3208 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.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 08:21:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:43: 1000000 INFO @ Tue, 16 Jun 2020 08:21:47: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:52: 3000000 INFO @ Tue, 16 Jun 2020 08:21:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:52: #1 total tags in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:21:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:52: #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 08:21:52: #1 tags after filtering in treatment: 3028283 INFO @ Tue, 16 Jun 2020 08:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:53: #2 number of paired peaks: 2179 INFO @ Tue, 16 Jun 2020 08:21:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:53: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:21:53: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20_model.r INFO @ Tue, 16 Jun 2020 08:21:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331088/SRX331088.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1919 records, 4 fields): 3 millis CompletedMACS2peakCalling