Job ID = 6367907 SRX = SRX4194200 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:07 prefetch.2.10.7: 1) Downloading 'SRR7291487'... 2020-06-15T23:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:48 prefetch.2.10.7: 'SRR7291487' is valid 2020-06-15T23:49:48 prefetch.2.10.7: 1) 'SRR7291487' was downloaded successfully 2020-06-15T23:49:48 prefetch.2.10.7: 'SRR7291487' has 0 unresolved dependencies Read 4998110 spots for SRR7291487/SRR7291487.sra Written 4998110 spots for SRR7291487/SRR7291487.sra 2020-06-15T23:50:20 prefetch.2.10.7: 1) Downloading 'SRR7291488'... 2020-06-15T23:50:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:16 prefetch.2.10.7: 'SRR7291488' is valid 2020-06-15T23:51:16 prefetch.2.10.7: 1) 'SRR7291488' was downloaded successfully 2020-06-15T23:51:16 prefetch.2.10.7: 'SRR7291488' has 0 unresolved dependencies Read 4879899 spots for SRR7291488/SRR7291488.sra Written 4879899 spots for SRR7291488/SRR7291488.sra 2020-06-15T23:51:44 prefetch.2.10.7: 1) Downloading 'SRR7291489'... 2020-06-15T23:51:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:40 prefetch.2.10.7: 'SRR7291489' is valid 2020-06-15T23:52:40 prefetch.2.10.7: 1) 'SRR7291489' was downloaded successfully 2020-06-15T23:52:40 prefetch.2.10.7: 'SRR7291489' has 0 unresolved dependencies Read 4984542 spots for SRR7291489/SRR7291489.sra Written 4984542 spots for SRR7291489/SRR7291489.sra 2020-06-15T23:53:11 prefetch.2.10.7: 1) Downloading 'SRR7291491'... 2020-06-15T23:53:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:06 prefetch.2.10.7: 'SRR7291491' is valid 2020-06-15T23:54:06 prefetch.2.10.7: 1) 'SRR7291491' was downloaded successfully 2020-06-15T23:54:06 prefetch.2.10.7: 'SRR7291491' has 0 unresolved dependencies Read 4828879 spots for SRR7291491/SRR7291491.sra Written 4828879 spots for SRR7291491/SRR7291491.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: 00:06:58 19691430 reads; of these: 19691430 (100.00%) were unpaired; of these: 271970 (1.38%) aligned 0 times 17227595 (87.49%) aligned exactly 1 time 2191865 (11.13%) aligned >1 times 98.62% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 3674813 / 19419460 = 0.1892 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 09:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.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 09:07:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:07: 1000000 INFO @ Tue, 16 Jun 2020 09:08:14: 2000000 INFO @ Tue, 16 Jun 2020 09:08:21: 3000000 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 09:08:28: 4000000 INFO @ Tue, 16 Jun 2020 09:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.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 09:08:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:36: 5000000 INFO @ Tue, 16 Jun 2020 09:08:38: 1000000 INFO @ Tue, 16 Jun 2020 09:08:45: 6000000 INFO @ Tue, 16 Jun 2020 09:08:46: 2000000 INFO @ Tue, 16 Jun 2020 09:08:53: 7000000 INFO @ Tue, 16 Jun 2020 09:08:54: 3000000 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 09:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.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 09:09:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:02: 8000000 INFO @ Tue, 16 Jun 2020 09:09:03: 4000000 INFO @ Tue, 16 Jun 2020 09:09:09: 1000000 INFO @ Tue, 16 Jun 2020 09:09:10: 9000000 INFO @ Tue, 16 Jun 2020 09:09:12: 5000000 INFO @ Tue, 16 Jun 2020 09:09:18: 2000000 INFO @ Tue, 16 Jun 2020 09:09:19: 10000000 INFO @ Tue, 16 Jun 2020 09:09:21: 6000000 INFO @ Tue, 16 Jun 2020 09:09:27: 3000000 INFO @ Tue, 16 Jun 2020 09:09:28: 11000000 INFO @ Tue, 16 Jun 2020 09:09:29: 7000000 INFO @ Tue, 16 Jun 2020 09:09:36: 4000000 INFO @ Tue, 16 Jun 2020 09:09:37: 12000000 INFO @ Tue, 16 Jun 2020 09:09:38: 8000000 INFO @ Tue, 16 Jun 2020 09:09:46: 5000000 INFO @ Tue, 16 Jun 2020 09:09:46: 13000000 INFO @ Tue, 16 Jun 2020 09:09:47: 9000000 INFO @ Tue, 16 Jun 2020 09:09:54: 14000000 INFO @ Tue, 16 Jun 2020 09:09:55: 6000000 INFO @ Tue, 16 Jun 2020 09:09:56: 10000000 INFO @ Tue, 16 Jun 2020 09:10:03: 15000000 INFO @ Tue, 16 Jun 2020 09:10:05: 7000000 INFO @ Tue, 16 Jun 2020 09:10:05: 11000000 INFO @ Tue, 16 Jun 2020 09:10:10: #1 tag size is determined as 73 bps INFO @ Tue, 16 Jun 2020 09:10:10: #1 tag size = 73 INFO @ Tue, 16 Jun 2020 09:10:10: #1 total tags in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:10:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:10: #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 09:10:10: #1 tags after filtering in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:11: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 09:10:11: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:12: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:10:12: #2 alternative fragment length(s) may be 3,105 bps INFO @ Tue, 16 Jun 2020 09:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:12: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:12: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Tue, 16 Jun 2020 09:10:12: #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 09:10:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:14: 8000000 INFO @ Tue, 16 Jun 2020 09:10:14: 12000000 INFO @ Tue, 16 Jun 2020 09:10:22: 9000000 INFO @ Tue, 16 Jun 2020 09:10:23: 13000000 INFO @ Tue, 16 Jun 2020 09:10:31: 10000000 INFO @ Tue, 16 Jun 2020 09:10:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:40: 11000000 INFO @ Tue, 16 Jun 2020 09:10:41: 15000000 INFO @ Tue, 16 Jun 2020 09:10:47: #1 tag size is determined as 73 bps INFO @ Tue, 16 Jun 2020 09:10:47: #1 tag size = 73 INFO @ Tue, 16 Jun 2020 09:10:47: #1 total tags in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:10:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:47: #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 09:10:47: #1 tags after filtering in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:49: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 09:10:49: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:49: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:10:49: #2 alternative fragment length(s) may be 3,105 bps INFO @ Tue, 16 Jun 2020 09:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:49: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:49: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Tue, 16 Jun 2020 09:10:49: #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 09:10:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:49: 12000000 INFO @ Tue, 16 Jun 2020 09:10:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:57: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:04: 14000000 INFO @ Tue, 16 Jun 2020 09:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9007 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:12: 15000000 INFO @ Tue, 16 Jun 2020 09:11:18: #1 tag size is determined as 73 bps INFO @ Tue, 16 Jun 2020 09:11:18: #1 tag size = 73 INFO @ Tue, 16 Jun 2020 09:11:18: #1 total tags in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:11:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:18: #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 09:11:18: #1 tags after filtering in treatment: 15744647 INFO @ Tue, 16 Jun 2020 09:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:19: #2 number of paired peaks: 594 WARNING @ Tue, 16 Jun 2020 09:11:19: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:20: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:11:20: #2 alternative fragment length(s) may be 3,105 bps INFO @ Tue, 16 Jun 2020 09:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:20: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:20: #2 You may need to consider one of the other alternative d(s): 3,105 WARNING @ Tue, 16 Jun 2020 09:11:20: #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 09:11:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3173 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194200/SRX4194200.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 1 millis CompletedMACS2peakCalling