Job ID = 6368066 SRX = SRX466529 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:54:33 prefetch.2.10.7: 1) Downloading 'SRR1163595'... 2020-06-15T23:54:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:27 prefetch.2.10.7: 1) 'SRR1163595' was downloaded successfully Read 13475705 spots for SRR1163595/SRR1163595.sra Written 13475705 spots for SRR1163595/SRR1163595.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: 00:03:14 13475705 reads; of these: 13475705 (100.00%) were unpaired; of these: 642942 (4.77%) aligned 0 times 7916867 (58.75%) aligned exactly 1 time 4915896 (36.48%) aligned >1 times 95.23% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 5624193 / 12832763 = 0.4383 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 09:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.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 09:04:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:32: 1000000 INFO @ Tue, 16 Jun 2020 09:04:38: 2000000 INFO @ Tue, 16 Jun 2020 09:04:45: 3000000 INFO @ Tue, 16 Jun 2020 09:04:51: 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 09:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.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 09:04:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:58: 5000000 INFO @ Tue, 16 Jun 2020 09:05:02: 1000000 INFO @ Tue, 16 Jun 2020 09:05:05: 6000000 INFO @ Tue, 16 Jun 2020 09:05:09: 2000000 INFO @ Tue, 16 Jun 2020 09:05:12: 7000000 INFO @ Tue, 16 Jun 2020 09:05:14: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:14: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:14: #1 total tags in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:05:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:14: #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 09:05:14: #1 tags after filtering in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:05:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:15: #2 number of paired peaks: 4568 INFO @ Tue, 16 Jun 2020 09:05:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:15: #2 predicted fragment length is 202 bps INFO @ Tue, 16 Jun 2020 09:05:15: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 16 Jun 2020 09:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05_model.r INFO @ Tue, 16 Jun 2020 09:05:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:16: 3000000 INFO @ Tue, 16 Jun 2020 09:05:22: 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 09:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.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 09:05:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:29: 5000000 INFO @ Tue, 16 Jun 2020 09:05:32: 1000000 INFO @ Tue, 16 Jun 2020 09:05:36: 6000000 INFO @ Tue, 16 Jun 2020 09:05:39: 2000000 INFO @ Tue, 16 Jun 2020 09:05:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:43: 7000000 INFO @ Tue, 16 Jun 2020 09:05:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:44: #1 total tags in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:05:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:44: #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 09:05:45: #1 tags after filtering in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:45: #2 number of paired peaks: 4568 INFO @ Tue, 16 Jun 2020 09:05:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:46: #2 predicted fragment length is 202 bps INFO @ Tue, 16 Jun 2020 09:05:46: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 16 Jun 2020 09:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10_model.r INFO @ Tue, 16 Jun 2020 09:05:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:46: 3000000 INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.05_summits.bed INFO @ Tue, 16 Jun 2020 09:05:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5750 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:59: 5000000 INFO @ Tue, 16 Jun 2020 09:06:05: 6000000 INFO @ Tue, 16 Jun 2020 09:06:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:12: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:06:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:06:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:06:13: #1 total tags in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:06:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:13: #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 09:06:13: #1 tags after filtering in treatment: 7208570 INFO @ Tue, 16 Jun 2020 09:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:14: #2 number of paired peaks: 4568 INFO @ Tue, 16 Jun 2020 09:06:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:14: #2 predicted fragment length is 202 bps INFO @ Tue, 16 Jun 2020 09:06:14: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 16 Jun 2020 09:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20_model.r INFO @ Tue, 16 Jun 2020 09:06:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.10_summits.bed INFO @ Tue, 16 Jun 2020 09:06:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3956 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466529/SRX466529.20_summits.bed INFO @ Tue, 16 Jun 2020 09:06:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2195 records, 4 fields): 3 millis CompletedMACS2peakCalling