Job ID = 6367745 SRX = SRX4082359 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:44 prefetch.2.10.7: 1) Downloading 'SRR7164177'... 2020-06-15T23:45:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:09 prefetch.2.10.7: 'SRR7164177' is valid 2020-06-15T23:47:09 prefetch.2.10.7: 1) 'SRR7164177' was downloaded successfully 2020-06-15T23:47:09 prefetch.2.10.7: 'SRR7164177' has 0 unresolved dependencies Read 12081024 spots for SRR7164177/SRR7164177.sra Written 12081024 spots for SRR7164177/SRR7164177.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: 00:02:46 12081024 reads; of these: 12081024 (100.00%) were unpaired; of these: 292065 (2.42%) aligned 0 times 10392363 (86.02%) aligned exactly 1 time 1396596 (11.56%) aligned >1 times 97.58% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 2679243 / 11788959 = 0.2273 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 08:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.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 08:53:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:43: 1000000 INFO @ Tue, 16 Jun 2020 08:53:48: 2000000 INFO @ Tue, 16 Jun 2020 08:53:54: 3000000 INFO @ Tue, 16 Jun 2020 08:53:59: 4000000 INFO @ Tue, 16 Jun 2020 08:54:05: 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 08:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.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 08:54:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:10: 6000000 INFO @ Tue, 16 Jun 2020 08:54:13: 1000000 INFO @ Tue, 16 Jun 2020 08:54:16: 7000000 INFO @ Tue, 16 Jun 2020 08:54:19: 2000000 INFO @ Tue, 16 Jun 2020 08:54:21: 8000000 INFO @ Tue, 16 Jun 2020 08:54:24: 3000000 INFO @ Tue, 16 Jun 2020 08:54:27: 9000000 INFO @ Tue, 16 Jun 2020 08:54:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:54:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:54:28: #1 total tags in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:54:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:28: #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 08:54:28: #1 tags after filtering in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:54:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:29: #2 number of paired peaks: 2585 INFO @ Tue, 16 Jun 2020 08:54:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:29: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:54:29: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 16 Jun 2020 08:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05_model.r INFO @ Tue, 16 Jun 2020 08:54:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:30: 4000000 INFO @ Tue, 16 Jun 2020 08:54:35: 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 08:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.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 08:54:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:41: 6000000 INFO @ Tue, 16 Jun 2020 08:54:44: 1000000 INFO @ Tue, 16 Jun 2020 08:54:46: 7000000 INFO @ Tue, 16 Jun 2020 08:54:50: 2000000 INFO @ Tue, 16 Jun 2020 08:54:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:52: 8000000 INFO @ Tue, 16 Jun 2020 08:54:57: 3000000 INFO @ Tue, 16 Jun 2020 08:54:58: 9000000 INFO @ Tue, 16 Jun 2020 08:54:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:54:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:54:59: #1 total tags in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:54:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:59: #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 08:54:59: #1 tags after filtering in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:54:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:00: #2 number of paired peaks: 2585 INFO @ Tue, 16 Jun 2020 08:55:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:00: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:55:00: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 16 Jun 2020 08:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10_model.r INFO @ Tue, 16 Jun 2020 08:55:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:03: 4000000 INFO @ Tue, 16 Jun 2020 08:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.05_summits.bed INFO @ Tue, 16 Jun 2020 08:55:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6732 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:09: 5000000 INFO @ Tue, 16 Jun 2020 08:55:15: 6000000 INFO @ Tue, 16 Jun 2020 08:55:21: 7000000 INFO @ Tue, 16 Jun 2020 08:55:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:55:27: 8000000 INFO @ Tue, 16 Jun 2020 08:55:33: 9000000 INFO @ Tue, 16 Jun 2020 08:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:34: #1 total tags in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:55:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:34: #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 08:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.10_summits.bed INFO @ Tue, 16 Jun 2020 08:55:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3454 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:34: #1 tags after filtering in treatment: 9109716 INFO @ Tue, 16 Jun 2020 08:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:35: #2 number of paired peaks: 2585 INFO @ Tue, 16 Jun 2020 08:55:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:35: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:55:35: #2 alternative fragment length(s) may be 4,155 bps INFO @ Tue, 16 Jun 2020 08:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20_model.r INFO @ Tue, 16 Jun 2020 08:55:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082359/SRX4082359.20_summits.bed INFO @ Tue, 16 Jun 2020 08:56:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 2 millis CompletedMACS2peakCalling