Job ID = 6366313 SRX = SRX1099840 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:31:29 prefetch.2.10.7: 1) Downloading 'SRR2105911'... 2020-06-15T22:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:23 prefetch.2.10.7: 'SRR2105911' is valid 2020-06-15T22:32:23 prefetch.2.10.7: 1) 'SRR2105911' was downloaded successfully Read 8044123 spots for SRR2105911/SRR2105911.sra Written 8044123 spots for SRR2105911/SRR2105911.sra 2020-06-15T22:32:56 prefetch.2.10.7: 1) Downloading 'SRR2105912'... 2020-06-15T22:32:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:12 prefetch.2.10.7: 'SRR2105912' is valid 2020-06-15T22:34:12 prefetch.2.10.7: 1) 'SRR2105912' was downloaded successfully Read 9962719 spots for SRR2105912/SRR2105912.sra Written 9962719 spots for SRR2105912/SRR2105912.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: 00:03:40 18006842 reads; of these: 18006842 (100.00%) were unpaired; of these: 1621723 (9.01%) aligned 0 times 14111948 (78.37%) aligned exactly 1 time 2273171 (12.62%) aligned >1 times 90.99% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 5988173 / 16385119 = 0.3655 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 07:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.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 07:42:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:37: 1000000 INFO @ Tue, 16 Jun 2020 07:42:43: 2000000 INFO @ Tue, 16 Jun 2020 07:42:49: 3000000 INFO @ Tue, 16 Jun 2020 07:42:55: 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 07:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.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 07:43:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:01: 5000000 INFO @ Tue, 16 Jun 2020 07:43:06: 1000000 INFO @ Tue, 16 Jun 2020 07:43:07: 6000000 INFO @ Tue, 16 Jun 2020 07:43:12: 2000000 INFO @ Tue, 16 Jun 2020 07:43:14: 7000000 INFO @ Tue, 16 Jun 2020 07:43:18: 3000000 INFO @ Tue, 16 Jun 2020 07:43:20: 8000000 INFO @ Tue, 16 Jun 2020 07:43:23: 4000000 INFO @ Tue, 16 Jun 2020 07:43:27: 9000000 INFO @ Tue, 16 Jun 2020 07:43:29: 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 07:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.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 07:43:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:33: 10000000 INFO @ Tue, 16 Jun 2020 07:43:34: 6000000 INFO @ Tue, 16 Jun 2020 07:43:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:35: #1 total tags in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:43:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:35: #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 07:43:36: #1 tags after filtering in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:36: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 07:43:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:36: #2 predicted fragment length is 201 bps INFO @ Tue, 16 Jun 2020 07:43:36: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 16 Jun 2020 07:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05_model.r INFO @ Tue, 16 Jun 2020 07:43:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:37: 1000000 INFO @ Tue, 16 Jun 2020 07:43:39: 7000000 INFO @ Tue, 16 Jun 2020 07:43:42: 2000000 INFO @ Tue, 16 Jun 2020 07:43:45: 8000000 INFO @ Tue, 16 Jun 2020 07:43:47: 3000000 INFO @ Tue, 16 Jun 2020 07:43:50: 9000000 INFO @ Tue, 16 Jun 2020 07:43:52: 4000000 INFO @ Tue, 16 Jun 2020 07:43:55: 10000000 INFO @ Tue, 16 Jun 2020 07:43:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:57: #1 total tags in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:43:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:57: #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 07:43:57: #1 tags after filtering in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:58: 5000000 INFO @ Tue, 16 Jun 2020 07:43:58: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 07:43:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:58: #2 predicted fragment length is 201 bps INFO @ Tue, 16 Jun 2020 07:43:58: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 16 Jun 2020 07:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10_model.r INFO @ Tue, 16 Jun 2020 07:43:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:03: 6000000 INFO @ Tue, 16 Jun 2020 07:44:08: 7000000 INFO @ Tue, 16 Jun 2020 07:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4542 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:13: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:18: 9000000 INFO @ Tue, 16 Jun 2020 07:44:23: 10000000 INFO @ Tue, 16 Jun 2020 07:44:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:25: #1 total tags in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:44:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:25: #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 07:44:25: #1 tags after filtering in treatment: 10396946 INFO @ Tue, 16 Jun 2020 07:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:26: #2 number of paired peaks: 1051 INFO @ Tue, 16 Jun 2020 07:44:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:26: #2 predicted fragment length is 201 bps INFO @ Tue, 16 Jun 2020 07:44:26: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 16 Jun 2020 07:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20_model.r INFO @ Tue, 16 Jun 2020 07:44:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2757 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1099840/SRX1099840.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1513 records, 4 fields): 3 millis CompletedMACS2peakCalling