Job ID = 6367629 SRX = SRX3583341 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:51 prefetch.2.10.7: 1) Downloading 'SRR6493997'... 2020-06-15T23:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:01 prefetch.2.10.7: 1) 'SRR6493997' was downloaded successfully 2020-06-15T23:33:01 prefetch.2.10.7: 'SRR6493997' has 0 unresolved dependencies Read 32777421 spots for SRR6493997/SRR6493997.sra Written 32777421 spots for SRR6493997/SRR6493997.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: 00:10:51 32777421 reads; of these: 32777421 (100.00%) were unpaired; of these: 710435 (2.17%) aligned 0 times 27923935 (85.19%) aligned exactly 1 time 4143051 (12.64%) aligned >1 times 97.83% overall alignment rate Time searching: 00:10:51 Overall time: 00:10:51 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 16 files... [bam_rmdupse_core] 6003377 / 32066986 = 0.1872 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 08:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.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 08:53:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:55: 1000000 INFO @ Tue, 16 Jun 2020 08:54:01: 2000000 INFO @ Tue, 16 Jun 2020 08:54:07: 3000000 INFO @ Tue, 16 Jun 2020 08:54:14: 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 08:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.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 08:54:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:20: 5000000 INFO @ Tue, 16 Jun 2020 08:54:26: 1000000 INFO @ Tue, 16 Jun 2020 08:54:27: 6000000 INFO @ Tue, 16 Jun 2020 08:54:33: 2000000 INFO @ Tue, 16 Jun 2020 08:54:34: 7000000 INFO @ Tue, 16 Jun 2020 08:54:40: 3000000 INFO @ Tue, 16 Jun 2020 08:54:41: 8000000 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 08:54:48: 4000000 INFO @ Tue, 16 Jun 2020 08:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.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 08:54:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:49: 9000000 INFO @ Tue, 16 Jun 2020 08:54:56: 5000000 INFO @ Tue, 16 Jun 2020 08:54:57: 10000000 INFO @ Tue, 16 Jun 2020 08:54:57: 1000000 INFO @ Tue, 16 Jun 2020 08:55:05: 6000000 INFO @ Tue, 16 Jun 2020 08:55:05: 11000000 INFO @ Tue, 16 Jun 2020 08:55:06: 2000000 INFO @ Tue, 16 Jun 2020 08:55:13: 7000000 INFO @ Tue, 16 Jun 2020 08:55:13: 12000000 INFO @ Tue, 16 Jun 2020 08:55:15: 3000000 INFO @ Tue, 16 Jun 2020 08:55:21: 13000000 INFO @ Tue, 16 Jun 2020 08:55:21: 8000000 INFO @ Tue, 16 Jun 2020 08:55:24: 4000000 INFO @ Tue, 16 Jun 2020 08:55:29: 14000000 INFO @ Tue, 16 Jun 2020 08:55:29: 9000000 INFO @ Tue, 16 Jun 2020 08:55:33: 5000000 INFO @ Tue, 16 Jun 2020 08:55:37: 15000000 INFO @ Tue, 16 Jun 2020 08:55:37: 10000000 INFO @ Tue, 16 Jun 2020 08:55:42: 6000000 INFO @ Tue, 16 Jun 2020 08:55:45: 16000000 INFO @ Tue, 16 Jun 2020 08:55:45: 11000000 INFO @ Tue, 16 Jun 2020 08:55:51: 7000000 INFO @ Tue, 16 Jun 2020 08:55:53: 17000000 INFO @ Tue, 16 Jun 2020 08:55:53: 12000000 INFO @ Tue, 16 Jun 2020 08:56:00: 8000000 INFO @ Tue, 16 Jun 2020 08:56:01: 18000000 INFO @ Tue, 16 Jun 2020 08:56:01: 13000000 INFO @ Tue, 16 Jun 2020 08:56:09: 9000000 INFO @ Tue, 16 Jun 2020 08:56:09: 19000000 INFO @ Tue, 16 Jun 2020 08:56:09: 14000000 INFO @ Tue, 16 Jun 2020 08:56:17: 20000000 INFO @ Tue, 16 Jun 2020 08:56:17: 15000000 INFO @ Tue, 16 Jun 2020 08:56:18: 10000000 INFO @ Tue, 16 Jun 2020 08:56:25: 21000000 INFO @ Tue, 16 Jun 2020 08:56:25: 16000000 INFO @ Tue, 16 Jun 2020 08:56:27: 11000000 INFO @ Tue, 16 Jun 2020 08:56:34: 22000000 INFO @ Tue, 16 Jun 2020 08:56:34: 17000000 INFO @ Tue, 16 Jun 2020 08:56:35: 12000000 INFO @ Tue, 16 Jun 2020 08:56:42: 23000000 INFO @ Tue, 16 Jun 2020 08:56:42: 18000000 INFO @ Tue, 16 Jun 2020 08:56:44: 13000000 INFO @ Tue, 16 Jun 2020 08:56:50: 24000000 INFO @ Tue, 16 Jun 2020 08:56:50: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:53: 14000000 INFO @ Tue, 16 Jun 2020 08:56:58: 25000000 INFO @ Tue, 16 Jun 2020 08:56:58: 20000000 INFO @ Tue, 16 Jun 2020 08:57:01: 15000000 INFO @ Tue, 16 Jun 2020 08:57:06: 26000000 INFO @ Tue, 16 Jun 2020 08:57:07: 21000000 INFO @ Tue, 16 Jun 2020 08:57:07: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:57:07: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:57:07: #1 total tags in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:57:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:07: #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 08:57:07: #1 tags after filtering in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:09: #2 number of paired peaks: 453 WARNING @ Tue, 16 Jun 2020 08:57:09: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:09: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:57:09: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 08:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05_model.r INFO @ Tue, 16 Jun 2020 08:57:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:10: 16000000 INFO @ Tue, 16 Jun 2020 08:57:15: 22000000 INFO @ Tue, 16 Jun 2020 08:57:19: 17000000 INFO @ Tue, 16 Jun 2020 08:57:22: 23000000 INFO @ Tue, 16 Jun 2020 08:57:28: 18000000 INFO @ Tue, 16 Jun 2020 08:57:30: 24000000 INFO @ Tue, 16 Jun 2020 08:57:37: 19000000 INFO @ Tue, 16 Jun 2020 08:57:38: 25000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:45: 20000000 INFO @ Tue, 16 Jun 2020 08:57:46: 26000000 INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:57:47: #1 total tags in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:57:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:47: #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 08:57:47: #1 tags after filtering in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:49: #2 number of paired peaks: 453 WARNING @ Tue, 16 Jun 2020 08:57:49: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:49: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:57:49: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 08:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10_model.r INFO @ Tue, 16 Jun 2020 08:57:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:54: 21000000 INFO @ Tue, 16 Jun 2020 08:57:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:02: 22000000 INFO @ Tue, 16 Jun 2020 08:58:10: 23000000 INFO @ Tue, 16 Jun 2020 08:58:18: 24000000 INFO @ Tue, 16 Jun 2020 08:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.05_summits.bed INFO @ Tue, 16 Jun 2020 08:58:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4804 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:26: 25000000 INFO @ Tue, 16 Jun 2020 08:58:33: 26000000 INFO @ Tue, 16 Jun 2020 08:58:34: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:58:34: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:58:34: #1 total tags in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:58:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:34: #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 08:58:34: #1 tags after filtering in treatment: 26063609 INFO @ Tue, 16 Jun 2020 08:58:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:36: #2 number of paired peaks: 453 WARNING @ Tue, 16 Jun 2020 08:58:36: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:36: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:58:36: #2 alternative fragment length(s) may be 4,162 bps INFO @ Tue, 16 Jun 2020 08:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20_model.r INFO @ Tue, 16 Jun 2020 08:58:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3719 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583341/SRX3583341.20_summits.bed INFO @ Tue, 16 Jun 2020 08:59:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2838 records, 4 fields): 4 millis CompletedMACS2peakCalling