Job ID = 6367747 SRX = SRX4082361 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:14 prefetch.2.10.7: 1) Downloading 'SRR7164179'... 2020-06-15T23:44:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:25 prefetch.2.10.7: 'SRR7164179' is valid 2020-06-15T23:46:25 prefetch.2.10.7: 1) 'SRR7164179' was downloaded successfully 2020-06-15T23:46:25 prefetch.2.10.7: 'SRR7164179' has 0 unresolved dependencies Read 18785774 spots for SRR7164179/SRR7164179.sra Written 18785774 spots for SRR7164179/SRR7164179.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: 00:04:25 18785774 reads; of these: 18785774 (100.00%) were unpaired; of these: 233175 (1.24%) aligned 0 times 16552834 (88.11%) aligned exactly 1 time 1999765 (10.65%) aligned >1 times 98.76% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 3529492 / 18552599 = 0.1902 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 08:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.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 08:56:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:42: 1000000 INFO @ Tue, 16 Jun 2020 08:56:47: 2000000 INFO @ Tue, 16 Jun 2020 08:56:52: 3000000 INFO @ Tue, 16 Jun 2020 08:56:57: 4000000 INFO @ Tue, 16 Jun 2020 08:57:02: 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 08:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.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 08:57:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:07: 6000000 INFO @ Tue, 16 Jun 2020 08:57:12: 1000000 INFO @ Tue, 16 Jun 2020 08:57:13: 7000000 INFO @ Tue, 16 Jun 2020 08:57:18: 2000000 INFO @ Tue, 16 Jun 2020 08:57:19: 8000000 INFO @ Tue, 16 Jun 2020 08:57:23: 3000000 INFO @ Tue, 16 Jun 2020 08:57:24: 9000000 INFO @ Tue, 16 Jun 2020 08:57:29: 4000000 INFO @ Tue, 16 Jun 2020 08:57:30: 10000000 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 08:57:35: 5000000 INFO @ Tue, 16 Jun 2020 08:57:35: 11000000 INFO @ Tue, 16 Jun 2020 08:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.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 08:57:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:40: 6000000 INFO @ Tue, 16 Jun 2020 08:57:41: 12000000 INFO @ Tue, 16 Jun 2020 08:57:42: 1000000 INFO @ Tue, 16 Jun 2020 08:57:46: 7000000 INFO @ Tue, 16 Jun 2020 08:57:47: 13000000 INFO @ Tue, 16 Jun 2020 08:57:48: 2000000 INFO @ Tue, 16 Jun 2020 08:57:52: 8000000 INFO @ Tue, 16 Jun 2020 08:57:53: 14000000 INFO @ Tue, 16 Jun 2020 08:57:54: 3000000 INFO @ Tue, 16 Jun 2020 08:57:58: 9000000 INFO @ Tue, 16 Jun 2020 08:57:59: 15000000 INFO @ Tue, 16 Jun 2020 08:57:59: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:57:59: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:57:59: #1 total tags in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:57:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:59: #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 08:57:59: #1 tags after filtering in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:00: 4000000 INFO @ Tue, 16 Jun 2020 08:58:00: #2 number of paired peaks: 2471 INFO @ Tue, 16 Jun 2020 08:58:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:00: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:58:00: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Tue, 16 Jun 2020 08:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05_model.r INFO @ Tue, 16 Jun 2020 08:58:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:03: 10000000 INFO @ Tue, 16 Jun 2020 08:58:05: 5000000 INFO @ Tue, 16 Jun 2020 08:58:09: 11000000 INFO @ Tue, 16 Jun 2020 08:58:11: 6000000 INFO @ Tue, 16 Jun 2020 08:58:15: 12000000 INFO @ Tue, 16 Jun 2020 08:58:17: 7000000 INFO @ Tue, 16 Jun 2020 08:58:20: 13000000 INFO @ Tue, 16 Jun 2020 08:58:23: 8000000 INFO @ Tue, 16 Jun 2020 08:58:26: 14000000 INFO @ Tue, 16 Jun 2020 08:58:28: 9000000 INFO @ Tue, 16 Jun 2020 08:58:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:32: 15000000 INFO @ Tue, 16 Jun 2020 08:58:32: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:58:32: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:58:32: #1 total tags in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:58:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:32: #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 08:58:32: #1 tags after filtering in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:33: #2 number of paired peaks: 2471 INFO @ Tue, 16 Jun 2020 08:58:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:34: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:58:34: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Tue, 16 Jun 2020 08:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10_model.r INFO @ Tue, 16 Jun 2020 08:58:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:34: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:39: 11000000 INFO @ Tue, 16 Jun 2020 08:58:44: 12000000 INFO @ Tue, 16 Jun 2020 08:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.05_summits.bed INFO @ Tue, 16 Jun 2020 08:58:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11070 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:50: 13000000 INFO @ Tue, 16 Jun 2020 08:58:55: 14000000 INFO @ Tue, 16 Jun 2020 08:59:00: 15000000 INFO @ Tue, 16 Jun 2020 08:59:00: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:59:00: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:59:00: #1 total tags in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:59:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:00: #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 08:59:00: #1 tags after filtering in treatment: 15023107 INFO @ Tue, 16 Jun 2020 08:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:00: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:59:02: #2 number of paired peaks: 2471 INFO @ Tue, 16 Jun 2020 08:59:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:02: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 08:59:02: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Tue, 16 Jun 2020 08:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20_model.r INFO @ Tue, 16 Jun 2020 08:59:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.10_summits.bed INFO @ Tue, 16 Jun 2020 08:59:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6541 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082361/SRX4082361.20_summits.bed INFO @ Tue, 16 Jun 2020 08:59:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2145 records, 4 fields): 3 millis CompletedMACS2peakCalling