Job ID = 6368904 SRX = SRX6720165 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:19 prefetch.2.10.7: 1) Downloading 'SRR9972865'... 2020-06-16T00:28:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:54 prefetch.2.10.7: 1) 'SRR9972865' was downloaded successfully Read 34218469 spots for SRR9972865/SRR9972865.sra Written 34218469 spots for SRR9972865/SRR9972865.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: 00:08:00 34218469 reads; of these: 34218469 (100.00%) were unpaired; of these: 1782693 (5.21%) aligned 0 times 26868649 (78.52%) aligned exactly 1 time 5567127 (16.27%) aligned >1 times 94.79% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 16439185 / 32435776 = 0.5068 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 09:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.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 09:48:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:36: 1000000 INFO @ Tue, 16 Jun 2020 09:48:43: 2000000 INFO @ Tue, 16 Jun 2020 09:48:49: 3000000 INFO @ Tue, 16 Jun 2020 09:48:56: 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 09:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.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 09:48:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:03: 5000000 INFO @ Tue, 16 Jun 2020 09:49:06: 1000000 INFO @ Tue, 16 Jun 2020 09:49:10: 6000000 INFO @ Tue, 16 Jun 2020 09:49:14: 2000000 INFO @ Tue, 16 Jun 2020 09:49:18: 7000000 INFO @ Tue, 16 Jun 2020 09:49:21: 3000000 INFO @ Tue, 16 Jun 2020 09:49:25: 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 09:49:28: 4000000 INFO @ Tue, 16 Jun 2020 09:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.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 09:49:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:32: 9000000 INFO @ Tue, 16 Jun 2020 09:49:36: 5000000 INFO @ Tue, 16 Jun 2020 09:49:37: 1000000 INFO @ Tue, 16 Jun 2020 09:49:40: 10000000 INFO @ Tue, 16 Jun 2020 09:49:43: 6000000 INFO @ Tue, 16 Jun 2020 09:49:44: 2000000 INFO @ Tue, 16 Jun 2020 09:49:47: 11000000 INFO @ Tue, 16 Jun 2020 09:49:51: 7000000 INFO @ Tue, 16 Jun 2020 09:49:51: 3000000 INFO @ Tue, 16 Jun 2020 09:49:55: 12000000 INFO @ Tue, 16 Jun 2020 09:49:58: 8000000 INFO @ Tue, 16 Jun 2020 09:49:59: 4000000 INFO @ Tue, 16 Jun 2020 09:50:02: 13000000 INFO @ Tue, 16 Jun 2020 09:50:06: 9000000 INFO @ Tue, 16 Jun 2020 09:50:06: 5000000 INFO @ Tue, 16 Jun 2020 09:50:10: 14000000 INFO @ Tue, 16 Jun 2020 09:50:13: 6000000 INFO @ Tue, 16 Jun 2020 09:50:13: 10000000 INFO @ Tue, 16 Jun 2020 09:50:17: 15000000 INFO @ Tue, 16 Jun 2020 09:50:20: 7000000 INFO @ Tue, 16 Jun 2020 09:50:21: 11000000 INFO @ Tue, 16 Jun 2020 09:50:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:25: #1 total tags in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:50:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:25: #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 09:50:25: #1 tags after filtering in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:50:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:26: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:50:26: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:27: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:50:27: #2 alternative fragment length(s) may be 1,33,36,578 bps INFO @ Tue, 16 Jun 2020 09:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:27: #2 You may need to consider one of the other alternative d(s): 1,33,36,578 WARNING @ Tue, 16 Jun 2020 09:50:27: #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 09:50:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:28: 8000000 INFO @ Tue, 16 Jun 2020 09:50:28: 12000000 INFO @ Tue, 16 Jun 2020 09:50:35: 9000000 INFO @ Tue, 16 Jun 2020 09:50:35: 13000000 INFO @ Tue, 16 Jun 2020 09:50:42: 10000000 INFO @ Tue, 16 Jun 2020 09:50:43: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:50: 11000000 INFO @ Tue, 16 Jun 2020 09:50:50: 15000000 INFO @ Tue, 16 Jun 2020 09:50:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:57: 12000000 INFO @ Tue, 16 Jun 2020 09:50:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:58: #1 total tags in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:50:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:58: #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 09:50:58: #1 tags after filtering in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:59: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:50:59: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:50:59: #2 alternative fragment length(s) may be 1,33,36,578 bps INFO @ Tue, 16 Jun 2020 09:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:59: #2 You may need to consider one of the other alternative d(s): 1,33,36,578 WARNING @ Tue, 16 Jun 2020 09:50:59: #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 09:50:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:04: 13000000 INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:09: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:11: 14000000 INFO @ Tue, 16 Jun 2020 09:51:19: 15000000 INFO @ Tue, 16 Jun 2020 09:51:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:26: #1 total tags in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:51:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:26: #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 09:51:26: #1 tags after filtering in treatment: 15996591 INFO @ Tue, 16 Jun 2020 09:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:27: #2 number of paired peaks: 433 WARNING @ Tue, 16 Jun 2020 09:51:27: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:28: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:51:28: #2 alternative fragment length(s) may be 1,33,36,578 bps INFO @ Tue, 16 Jun 2020 09:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:28: #2 You may need to consider one of the other alternative d(s): 1,33,36,578 WARNING @ Tue, 16 Jun 2020 09:51:28: #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 09:51:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:42: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720165/SRX6720165.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling