Job ID = 6367682 SRX = SRX3883437 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR6938934'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:22 prefetch.2.10.7: 'SRR6938934' is valid 2020-06-15T23:34:22 prefetch.2.10.7: 1) 'SRR6938934' was downloaded successfully 2020-06-15T23:34:22 prefetch.2.10.7: 'SRR6938934' has 0 unresolved dependencies Read 10754778 spots for SRR6938934/SRR6938934.sra Written 10754778 spots for SRR6938934/SRR6938934.sra 2020-06-15T23:35:05 prefetch.2.10.7: 1) Downloading 'SRR6938935'... 2020-06-15T23:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:45 prefetch.2.10.7: 'SRR6938935' is valid 2020-06-15T23:37:45 prefetch.2.10.7: 1) 'SRR6938935' was downloaded successfully 2020-06-15T23:37:45 prefetch.2.10.7: 'SRR6938935' has 0 unresolved dependencies Read 20858613 spots for SRR6938935/SRR6938935.sra Written 20858613 spots for SRR6938935/SRR6938935.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: 00:04:28 31613391 reads; of these: 31613391 (100.00%) were unpaired; of these: 18646690 (58.98%) aligned 0 times 10704089 (33.86%) aligned exactly 1 time 2262612 (7.16%) aligned >1 times 41.02% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 2150160 / 12966701 = 0.1658 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 08:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.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 08:46:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:43: 1000000 INFO @ Tue, 16 Jun 2020 08:46:47: 2000000 INFO @ Tue, 16 Jun 2020 08:46:52: 3000000 INFO @ Tue, 16 Jun 2020 08:46:56: 4000000 INFO @ Tue, 16 Jun 2020 08:47:01: 5000000 INFO @ Tue, 16 Jun 2020 08:47:06: 6000000 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 08:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.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 08:47:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:10: 7000000 INFO @ Tue, 16 Jun 2020 08:47:13: 1000000 INFO @ Tue, 16 Jun 2020 08:47:15: 8000000 INFO @ Tue, 16 Jun 2020 08:47:19: 2000000 INFO @ Tue, 16 Jun 2020 08:47:20: 9000000 INFO @ Tue, 16 Jun 2020 08:47:25: 3000000 INFO @ Tue, 16 Jun 2020 08:47:25: 10000000 INFO @ Tue, 16 Jun 2020 08:47:29: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:47:29: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:47:29: #1 total tags in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:47:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:29: #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 08:47:29: #1 tags after filtering in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:30: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:47:30: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:30: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:47:30: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 16 Jun 2020 08:47:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:30: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 16 Jun 2020 08:47:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:47:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:30: 4000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:47:36: 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 08:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.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 08:47:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:41: 6000000 INFO @ Tue, 16 Jun 2020 08:47:42: 1000000 INFO @ Tue, 16 Jun 2020 08:47:47: 7000000 INFO @ Tue, 16 Jun 2020 08:47:47: 2000000 INFO @ Tue, 16 Jun 2020 08:47:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:53: 3000000 INFO @ Tue, 16 Jun 2020 08:47:53: 8000000 INFO @ Tue, 16 Jun 2020 08:47:58: 4000000 INFO @ Tue, 16 Jun 2020 08:47:58: 9000000 INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:02: 5000000 INFO @ Tue, 16 Jun 2020 08:48:04: 10000000 INFO @ Tue, 16 Jun 2020 08:48:07: 6000000 INFO @ Tue, 16 Jun 2020 08:48:09: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:48:09: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:48:09: #1 total tags in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:48:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:09: #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 08:48:09: #1 tags after filtering in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:48:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:10: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:48:10: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:10: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:48:10: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 16 Jun 2020 08:48:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:10: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 16 Jun 2020 08:48:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:48:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:12: 7000000 INFO @ Tue, 16 Jun 2020 08:48:17: 8000000 INFO @ Tue, 16 Jun 2020 08:48:22: 9000000 INFO @ Tue, 16 Jun 2020 08:48:26: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:30: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:48:30: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:48:30: #1 total tags in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:48:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:30: #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 08:48:31: #1 tags after filtering in treatment: 10816541 INFO @ Tue, 16 Jun 2020 08:48:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:31: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:48:31: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:31: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:48:31: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 16 Jun 2020 08:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:31: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:31: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 16 Jun 2020 08:48:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:48:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3883437/SRX3883437.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling