Job ID = 6367899 SRX = SRX4194190 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:03 prefetch.2.10.7: 1) Downloading 'SRR7291454'... 2020-06-15T23:46:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:17 prefetch.2.10.7: 'SRR7291454' is valid 2020-06-15T23:47:17 prefetch.2.10.7: 1) 'SRR7291454' was downloaded successfully 2020-06-15T23:47:17 prefetch.2.10.7: 'SRR7291454' has 0 unresolved dependencies Read 5403813 spots for SRR7291454/SRR7291454.sra Written 5403813 spots for SRR7291454/SRR7291454.sra 2020-06-15T23:47:50 prefetch.2.10.7: 1) Downloading 'SRR7291455'... 2020-06-15T23:47:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:57 prefetch.2.10.7: 'SRR7291455' is valid 2020-06-15T23:48:57 prefetch.2.10.7: 1) 'SRR7291455' was downloaded successfully 2020-06-15T23:48:57 prefetch.2.10.7: 'SRR7291455' has 0 unresolved dependencies Read 5276157 spots for SRR7291455/SRR7291455.sra Written 5276157 spots for SRR7291455/SRR7291455.sra 2020-06-15T23:49:31 prefetch.2.10.7: 1) Downloading 'SRR7291456'... 2020-06-15T23:49:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:17 prefetch.2.10.7: 'SRR7291456' is valid 2020-06-15T23:50:17 prefetch.2.10.7: 1) 'SRR7291456' was downloaded successfully 2020-06-15T23:50:17 prefetch.2.10.7: 'SRR7291456' has 0 unresolved dependencies Read 5397633 spots for SRR7291456/SRR7291456.sra Written 5397633 spots for SRR7291456/SRR7291456.sra 2020-06-15T23:50:51 prefetch.2.10.7: 1) Downloading 'SRR7291457'... 2020-06-15T23:50:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:42 prefetch.2.10.7: 'SRR7291457' is valid 2020-06-15T23:51:42 prefetch.2.10.7: 1) 'SRR7291457' was downloaded successfully 2020-06-15T23:51:42 prefetch.2.10.7: 'SRR7291457' has 0 unresolved dependencies Read 5220958 spots for SRR7291457/SRR7291457.sra Written 5220958 spots for SRR7291457/SRR7291457.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: 00:08:41 21298561 reads; of these: 21298561 (100.00%) were unpaired; of these: 814312 (3.82%) aligned 0 times 15585005 (73.17%) aligned exactly 1 time 4899244 (23.00%) aligned >1 times 96.18% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 12 files... [bam_rmdupse_core] 3981040 / 20484249 = 0.1943 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 09:07:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.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 09:07:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:57: 1000000 INFO @ Tue, 16 Jun 2020 09:08:04: 2000000 INFO @ Tue, 16 Jun 2020 09:08:12: 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 09:08:19: 4000000 INFO @ Tue, 16 Jun 2020 09:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.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 09:08:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:27: 5000000 INFO @ Tue, 16 Jun 2020 09:08:28: 1000000 INFO @ Tue, 16 Jun 2020 09:08:35: 6000000 INFO @ Tue, 16 Jun 2020 09:08:37: 2000000 INFO @ Tue, 16 Jun 2020 09:08:43: 7000000 INFO @ Tue, 16 Jun 2020 09:08:46: 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 09:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.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 09:08:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:52: 8000000 INFO @ Tue, 16 Jun 2020 09:08:54: 4000000 INFO @ Tue, 16 Jun 2020 09:08:59: 1000000 INFO @ Tue, 16 Jun 2020 09:09:00: 9000000 INFO @ Tue, 16 Jun 2020 09:09:04: 5000000 INFO @ Tue, 16 Jun 2020 09:09:09: 2000000 INFO @ Tue, 16 Jun 2020 09:09:10: 10000000 INFO @ Tue, 16 Jun 2020 09:09:14: 6000000 INFO @ Tue, 16 Jun 2020 09:09:19: 11000000 INFO @ Tue, 16 Jun 2020 09:09:19: 3000000 INFO @ Tue, 16 Jun 2020 09:09:23: 7000000 INFO @ Tue, 16 Jun 2020 09:09:28: 4000000 INFO @ Tue, 16 Jun 2020 09:09:28: 12000000 INFO @ Tue, 16 Jun 2020 09:09:32: 8000000 INFO @ Tue, 16 Jun 2020 09:09:37: 5000000 INFO @ Tue, 16 Jun 2020 09:09:37: 13000000 INFO @ Tue, 16 Jun 2020 09:09:42: 9000000 INFO @ Tue, 16 Jun 2020 09:09:46: 6000000 INFO @ Tue, 16 Jun 2020 09:09:46: 14000000 INFO @ Tue, 16 Jun 2020 09:09:51: 10000000 INFO @ Tue, 16 Jun 2020 09:09:55: 7000000 INFO @ Tue, 16 Jun 2020 09:09:56: 15000000 INFO @ Tue, 16 Jun 2020 09:10:00: 11000000 INFO @ Tue, 16 Jun 2020 09:10:05: 8000000 INFO @ Tue, 16 Jun 2020 09:10:05: 16000000 INFO @ Tue, 16 Jun 2020 09:10:09: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:10:09: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:10:09: #1 total tags in treatment: 16503209 INFO @ Tue, 16 Jun 2020 09:10:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:09: #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 09:10:10: 12000000 INFO @ Tue, 16 Jun 2020 09:10:10: #1 tags after filtering in treatment: 16503209 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: 472 WARNING @ Tue, 16 Jun 2020 09:10:11: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:11: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:10:11: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 16 Jun 2020 09:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:11: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 16 Jun 2020 09:10:11: #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 09:10:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:14: 9000000 INFO @ Tue, 16 Jun 2020 09:10:19: 13000000 INFO @ Tue, 16 Jun 2020 09:10:23: 10000000 INFO @ Tue, 16 Jun 2020 09:10:28: 14000000 INFO @ Tue, 16 Jun 2020 09:10:32: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:38: 15000000 INFO @ Tue, 16 Jun 2020 09:10:42: 12000000 INFO @ Tue, 16 Jun 2020 09:10:47: 16000000 INFO @ Tue, 16 Jun 2020 09:10:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:51: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:10:51: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:10:51: #1 total tags in treatment: 16503209 INFO @ Tue, 16 Jun 2020 09:10:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:51: #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 09:10:51: 13000000 INFO @ Tue, 16 Jun 2020 09:10:51: #1 tags after filtering in treatment: 16503209 INFO @ Tue, 16 Jun 2020 09:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:53: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 09:10:53: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:53: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:10:53: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 16 Jun 2020 09:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:53: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 16 Jun 2020 09:10:53: #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 09:10:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:00: 14000000 INFO @ Tue, 16 Jun 2020 09:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (941 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:08: 15000000 INFO @ Tue, 16 Jun 2020 09:11:16: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:20: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:11:20: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:11:20: #1 total tags in treatment: 16503209 INFO @ Tue, 16 Jun 2020 09:11:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:20: #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 09:11:20: #1 tags after filtering in treatment: 16503209 INFO @ Tue, 16 Jun 2020 09:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:22: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 09:11:22: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:22: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:11:22: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 16 Jun 2020 09:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:22: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 16 Jun 2020 09:11:22: #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 09:11:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (606 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194190/SRX4194190.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 1 millis CompletedMACS2peakCalling