Job ID = 14160706 SRX = SRX10399013 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:31 26032717 reads; of these: 26032717 (100.00%) were unpaired; of these: 5943131 (22.83%) aligned 0 times 16867744 (64.79%) aligned exactly 1 time 3221842 (12.38%) aligned >1 times 77.17% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 3212386 / 20089586 = 0.1599 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 04:01:35: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:01:35: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:01:43: 1000000 INFO @ Thu, 09 Dec 2021 04:01:50: 2000000 INFO @ Thu, 09 Dec 2021 04:01:57: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:02:05: 4000000 INFO @ Thu, 09 Dec 2021 04:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 04:02:05: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:02:05: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:02:13: 1000000 INFO @ Thu, 09 Dec 2021 04:02:13: 5000000 INFO @ Thu, 09 Dec 2021 04:02:21: 2000000 INFO @ Thu, 09 Dec 2021 04:02:22: 6000000 INFO @ Thu, 09 Dec 2021 04:02:28: 3000000 INFO @ Thu, 09 Dec 2021 04:02:30: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:02:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.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 @ Thu, 09 Dec 2021 04:02:35: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:02:35: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:02:36: 4000000 INFO @ Thu, 09 Dec 2021 04:02:38: 8000000 INFO @ Thu, 09 Dec 2021 04:02:43: 1000000 INFO @ Thu, 09 Dec 2021 04:02:43: 5000000 INFO @ Thu, 09 Dec 2021 04:02:46: 9000000 INFO @ Thu, 09 Dec 2021 04:02:51: 2000000 INFO @ Thu, 09 Dec 2021 04:02:51: 6000000 INFO @ Thu, 09 Dec 2021 04:02:55: 10000000 INFO @ Thu, 09 Dec 2021 04:02:58: 3000000 INFO @ Thu, 09 Dec 2021 04:02:59: 7000000 INFO @ Thu, 09 Dec 2021 04:03:03: 11000000 INFO @ Thu, 09 Dec 2021 04:03:06: 4000000 INFO @ Thu, 09 Dec 2021 04:03:06: 8000000 INFO @ Thu, 09 Dec 2021 04:03:11: 12000000 INFO @ Thu, 09 Dec 2021 04:03:13: 5000000 INFO @ Thu, 09 Dec 2021 04:03:14: 9000000 INFO @ Thu, 09 Dec 2021 04:03:20: 13000000 INFO @ Thu, 09 Dec 2021 04:03:21: 6000000 INFO @ Thu, 09 Dec 2021 04:03:22: 10000000 INFO @ Thu, 09 Dec 2021 04:03:28: 14000000 INFO @ Thu, 09 Dec 2021 04:03:29: 7000000 INFO @ Thu, 09 Dec 2021 04:03:29: 11000000 INFO @ Thu, 09 Dec 2021 04:03:36: 8000000 INFO @ Thu, 09 Dec 2021 04:03:36: 15000000 INFO @ Thu, 09 Dec 2021 04:03:37: 12000000 INFO @ Thu, 09 Dec 2021 04:03:44: 9000000 INFO @ Thu, 09 Dec 2021 04:03:44: 13000000 INFO @ Thu, 09 Dec 2021 04:03:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:03:51: 10000000 INFO @ Thu, 09 Dec 2021 04:03:52: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:03:52: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:03:52: #1 total tags in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:03:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:03:52: 14000000 INFO @ Thu, 09 Dec 2021 04:03:52: #1 tags after filtering in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:03:52: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:53: #2 number of paired peaks: 350 WARNING @ Thu, 09 Dec 2021 04:03:53: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:53: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:53: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:53: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:53: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:53: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 04:03:53: #2 alternative fragment length(s) may be 4,110 bps INFO @ Thu, 09 Dec 2021 04:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05_model.r WARNING @ Thu, 09 Dec 2021 04:03:53: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:03:53: #2 You may need to consider one of the other alternative d(s): 4,110 WARNING @ Thu, 09 Dec 2021 04:03:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:03:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:59: 11000000 INFO @ Thu, 09 Dec 2021 04:03:59: 15000000 INFO @ Thu, 09 Dec 2021 04:04:06: 12000000 INFO @ Thu, 09 Dec 2021 04:04:06: 16000000 INFO @ Thu, 09 Dec 2021 04:04:13: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:04:13: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:04:13: #1 total tags in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:04:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:04:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:04:13: #1 tags after filtering in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:04:13: #1 finished! INFO @ Thu, 09 Dec 2021 04:04:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:04:13: 13000000 INFO @ Thu, 09 Dec 2021 04:04:14: #2 number of paired peaks: 350 WARNING @ Thu, 09 Dec 2021 04:04:14: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Thu, 09 Dec 2021 04:04:14: start model_add_line... INFO @ Thu, 09 Dec 2021 04:04:14: start X-correlation... INFO @ Thu, 09 Dec 2021 04:04:14: end of X-cor INFO @ Thu, 09 Dec 2021 04:04:14: #2 finished! INFO @ Thu, 09 Dec 2021 04:04:14: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 04:04:14: #2 alternative fragment length(s) may be 4,110 bps INFO @ Thu, 09 Dec 2021 04:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10_model.r WARNING @ Thu, 09 Dec 2021 04:04:14: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:04:14: #2 You may need to consider one of the other alternative d(s): 4,110 WARNING @ Thu, 09 Dec 2021 04:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:04:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:04:20: 14000000 INFO @ Thu, 09 Dec 2021 04:04:26: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:04:27: 15000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:04:34: 16000000 INFO @ Thu, 09 Dec 2021 04:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.05_summits.bed INFO @ Thu, 09 Dec 2021 04:04:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2163 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:04:44: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:04:44: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:04:44: #1 total tags in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:04:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:04:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:04:44: #1 tags after filtering in treatment: 16877200 INFO @ Thu, 09 Dec 2021 04:04:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:04:44: #1 finished! INFO @ Thu, 09 Dec 2021 04:04:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:04:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:04:46: #2 number of paired peaks: 350 WARNING @ Thu, 09 Dec 2021 04:04:46: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Thu, 09 Dec 2021 04:04:46: start model_add_line... INFO @ Thu, 09 Dec 2021 04:04:46: start X-correlation... INFO @ Thu, 09 Dec 2021 04:04:46: end of X-cor INFO @ Thu, 09 Dec 2021 04:04:46: #2 finished! INFO @ Thu, 09 Dec 2021 04:04:46: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 04:04:46: #2 alternative fragment length(s) may be 4,110 bps INFO @ Thu, 09 Dec 2021 04:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20_model.r WARNING @ Thu, 09 Dec 2021 04:04:46: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:04:46: #2 You may need to consider one of the other alternative d(s): 4,110 WARNING @ Thu, 09 Dec 2021 04:04:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:04:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:04:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:05:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:05:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.10_summits.bed INFO @ Thu, 09 Dec 2021 04:05:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:05:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399013/SRX10399013.20_summits.bed INFO @ Thu, 09 Dec 2021 04:05:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (840 records, 4 fields): 3 millis CompletedMACS2peakCalling