Job ID = 6368982 SRX = SRX7971807 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:17 prefetch.2.10.7: 1) Downloading 'SRR11392693'... 2020-06-16T00:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:57 prefetch.2.10.7: 1) 'SRR11392693' was downloaded successfully Read 28017931 spots for SRR11392693/SRR11392693.sra Written 28017931 spots for SRR11392693/SRR11392693.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: 00:09:52 28017931 reads; of these: 28017931 (100.00%) were unpaired; of these: 694902 (2.48%) aligned 0 times 20902402 (74.60%) aligned exactly 1 time 6420627 (22.92%) aligned >1 times 97.52% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 5562754 / 27323029 = 0.2036 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 10:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.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 10:05:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:10: 1000000 INFO @ Tue, 16 Jun 2020 10:05:17: 2000000 INFO @ Tue, 16 Jun 2020 10:05:24: 3000000 INFO @ Tue, 16 Jun 2020 10:05:31: 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 10:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.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 10:05:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:38: 5000000 INFO @ Tue, 16 Jun 2020 10:05:41: 1000000 INFO @ Tue, 16 Jun 2020 10:05:47: 6000000 INFO @ Tue, 16 Jun 2020 10:05:50: 2000000 INFO @ Tue, 16 Jun 2020 10:05:55: 7000000 INFO @ Tue, 16 Jun 2020 10:05:58: 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 10:06:03: 8000000 INFO @ Tue, 16 Jun 2020 10:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.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 10:06:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:06:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:06:07: 4000000 INFO @ Tue, 16 Jun 2020 10:06:11: 9000000 INFO @ Tue, 16 Jun 2020 10:06:11: 1000000 INFO @ Tue, 16 Jun 2020 10:06:15: 5000000 INFO @ Tue, 16 Jun 2020 10:06:19: 10000000 INFO @ Tue, 16 Jun 2020 10:06:20: 2000000 INFO @ Tue, 16 Jun 2020 10:06:24: 6000000 INFO @ Tue, 16 Jun 2020 10:06:28: 11000000 INFO @ Tue, 16 Jun 2020 10:06:28: 3000000 INFO @ Tue, 16 Jun 2020 10:06:33: 7000000 INFO @ Tue, 16 Jun 2020 10:06:36: 12000000 INFO @ Tue, 16 Jun 2020 10:06:37: 4000000 INFO @ Tue, 16 Jun 2020 10:06:42: 8000000 INFO @ Tue, 16 Jun 2020 10:06:44: 13000000 INFO @ Tue, 16 Jun 2020 10:06:45: 5000000 INFO @ Tue, 16 Jun 2020 10:06:51: 9000000 INFO @ Tue, 16 Jun 2020 10:06:53: 14000000 INFO @ Tue, 16 Jun 2020 10:06:54: 6000000 INFO @ Tue, 16 Jun 2020 10:06:59: 10000000 INFO @ Tue, 16 Jun 2020 10:07:01: 15000000 INFO @ Tue, 16 Jun 2020 10:07:02: 7000000 INFO @ Tue, 16 Jun 2020 10:07:08: 11000000 INFO @ Tue, 16 Jun 2020 10:07:10: 16000000 INFO @ Tue, 16 Jun 2020 10:07:11: 8000000 INFO @ Tue, 16 Jun 2020 10:07:17: 12000000 INFO @ Tue, 16 Jun 2020 10:07:18: 17000000 INFO @ Tue, 16 Jun 2020 10:07:19: 9000000 INFO @ Tue, 16 Jun 2020 10:07:26: 13000000 INFO @ Tue, 16 Jun 2020 10:07:27: 18000000 INFO @ Tue, 16 Jun 2020 10:07:28: 10000000 INFO @ Tue, 16 Jun 2020 10:07:34: 14000000 INFO @ Tue, 16 Jun 2020 10:07:35: 19000000 INFO @ Tue, 16 Jun 2020 10:07:36: 11000000 INFO @ Tue, 16 Jun 2020 10:07:43: 15000000 INFO @ Tue, 16 Jun 2020 10:07:44: 20000000 INFO @ Tue, 16 Jun 2020 10:07:45: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:07:52: 16000000 INFO @ Tue, 16 Jun 2020 10:07:53: 21000000 INFO @ Tue, 16 Jun 2020 10:07:54: 13000000 INFO @ Tue, 16 Jun 2020 10:07:59: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:07:59: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:07:59: #1 total tags in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:07:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:07:59: #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 10:08:00: #1 tags after filtering in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:08:00: #1 finished! INFO @ Tue, 16 Jun 2020 10:08:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:08:01: 17000000 INFO @ Tue, 16 Jun 2020 10:08:01: #2 number of paired peaks: 287 WARNING @ Tue, 16 Jun 2020 10:08:01: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 16 Jun 2020 10:08:01: start model_add_line... INFO @ Tue, 16 Jun 2020 10:08:01: start X-correlation... INFO @ Tue, 16 Jun 2020 10:08:01: end of X-cor INFO @ Tue, 16 Jun 2020 10:08:01: #2 finished! INFO @ Tue, 16 Jun 2020 10:08:01: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 10:08:01: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 10:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05_model.r WARNING @ Tue, 16 Jun 2020 10:08:01: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:08:01: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 10:08:01: #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 10:08:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:08:02: 14000000 INFO @ Tue, 16 Jun 2020 10:08:10: 18000000 INFO @ Tue, 16 Jun 2020 10:08:11: 15000000 INFO @ Tue, 16 Jun 2020 10:08:19: 19000000 INFO @ Tue, 16 Jun 2020 10:08:19: 16000000 INFO @ Tue, 16 Jun 2020 10:08:28: 17000000 INFO @ Tue, 16 Jun 2020 10:08:28: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:08:36: 18000000 INFO @ Tue, 16 Jun 2020 10:08:37: 21000000 INFO @ Tue, 16 Jun 2020 10:08:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:08:44: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:08:44: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:08:44: #1 total tags in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:08:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:08:44: #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 10:08:45: #1 tags after filtering in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:08:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:08:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:08:45: 19000000 INFO @ Tue, 16 Jun 2020 10:08:46: #2 number of paired peaks: 287 WARNING @ Tue, 16 Jun 2020 10:08:46: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 16 Jun 2020 10:08:46: start model_add_line... INFO @ Tue, 16 Jun 2020 10:08:46: start X-correlation... INFO @ Tue, 16 Jun 2020 10:08:46: end of X-cor INFO @ Tue, 16 Jun 2020 10:08:46: #2 finished! INFO @ Tue, 16 Jun 2020 10:08:46: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 10:08:46: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 10:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10_model.r WARNING @ Tue, 16 Jun 2020 10:08:46: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:08:46: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 10:08:46: #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 10:08:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:08:52: 20000000 INFO @ Tue, 16 Jun 2020 10:09:00: 21000000 INFO @ Tue, 16 Jun 2020 10:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.05_summits.bed INFO @ Tue, 16 Jun 2020 10:09:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:09:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:09:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:09:05: #1 total tags in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:09:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:09:05: #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 10:09:06: #1 tags after filtering in treatment: 21760275 INFO @ Tue, 16 Jun 2020 10:09:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:09:06: #1 finished! INFO @ Tue, 16 Jun 2020 10:09:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:09:07: #2 number of paired peaks: 287 WARNING @ Tue, 16 Jun 2020 10:09:07: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 16 Jun 2020 10:09:07: start model_add_line... INFO @ Tue, 16 Jun 2020 10:09:07: start X-correlation... INFO @ Tue, 16 Jun 2020 10:09:07: end of X-cor INFO @ Tue, 16 Jun 2020 10:09:07: #2 finished! INFO @ Tue, 16 Jun 2020 10:09:07: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 10:09:07: #2 alternative fragment length(s) may be 2,53,571 bps INFO @ Tue, 16 Jun 2020 10:09:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20_model.r WARNING @ Tue, 16 Jun 2020 10:09:07: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:09:07: #2 You may need to consider one of the other alternative d(s): 2,53,571 WARNING @ Tue, 16 Jun 2020 10:09:07: #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 10:09:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:09:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:09:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:09:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.10_summits.bed INFO @ Tue, 16 Jun 2020 10:09:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971807/SRX7971807.20_summits.bed INFO @ Tue, 16 Jun 2020 10:10:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (162 records, 4 fields): 2 millis CompletedMACS2peakCalling