Job ID = 14159566 SRX = SRX3180826 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: 00:03:44 14784189 reads; of these: 14784189 (100.00%) were unpaired; of these: 1406442 (9.51%) aligned 0 times 10393335 (70.30%) aligned exactly 1 time 2984412 (20.19%) aligned >1 times 90.49% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 2770729 / 13377747 = 0.2071 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 @ Wed, 08 Dec 2021 22:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 22:42:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:42:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:42:44: 1000000 INFO @ Wed, 08 Dec 2021 22:42:53: 2000000 INFO @ Wed, 08 Dec 2021 22:43:02: 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 @ Wed, 08 Dec 2021 22:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 22:43:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:43:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:43:11: 4000000 INFO @ Wed, 08 Dec 2021 22:43:16: 1000000 INFO @ Wed, 08 Dec 2021 22:43:21: 5000000 INFO @ Wed, 08 Dec 2021 22:43:26: 2000000 INFO @ Wed, 08 Dec 2021 22:43:30: 6000000 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 @ Wed, 08 Dec 2021 22:43:35: 3000000 INFO @ Wed, 08 Dec 2021 22:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 22:43:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:43:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:43:39: 7000000 INFO @ Wed, 08 Dec 2021 22:43:44: 4000000 INFO @ Wed, 08 Dec 2021 22:43:46: 1000000 INFO @ Wed, 08 Dec 2021 22:43:49: 8000000 INFO @ Wed, 08 Dec 2021 22:43:53: 5000000 INFO @ Wed, 08 Dec 2021 22:43:57: 2000000 INFO @ Wed, 08 Dec 2021 22:43:58: 9000000 INFO @ Wed, 08 Dec 2021 22:44:03: 6000000 INFO @ Wed, 08 Dec 2021 22:44:07: 10000000 INFO @ Wed, 08 Dec 2021 22:44:08: 3000000 INFO @ Wed, 08 Dec 2021 22:44:13: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:44:13: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:44:13: #1 total tags in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:44:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:44:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:44:13: #1 tags after filtering in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:44:13: #1 finished! INFO @ Wed, 08 Dec 2021 22:44:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:44:13: 7000000 INFO @ Wed, 08 Dec 2021 22:44:13: #2 number of paired peaks: 483 WARNING @ Wed, 08 Dec 2021 22:44:13: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Wed, 08 Dec 2021 22:44:13: start model_add_line... INFO @ Wed, 08 Dec 2021 22:44:14: start X-correlation... INFO @ Wed, 08 Dec 2021 22:44:14: end of X-cor INFO @ Wed, 08 Dec 2021 22:44:14: #2 finished! INFO @ Wed, 08 Dec 2021 22:44:14: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:44:14: #2 alternative fragment length(s) may be 2,47,569 bps INFO @ Wed, 08 Dec 2021 22:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05_model.r WARNING @ Wed, 08 Dec 2021 22:44:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:44:14: #2 You may need to consider one of the other alternative d(s): 2,47,569 WARNING @ Wed, 08 Dec 2021 22:44:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:44:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:44:19: 4000000 INFO @ Wed, 08 Dec 2021 22:44:23: 8000000 INFO @ Wed, 08 Dec 2021 22:44:29: 5000000 INFO @ Wed, 08 Dec 2021 22:44:32: 9000000 INFO @ Wed, 08 Dec 2021 22:44:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:44:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:44:42: 10000000 INFO @ Wed, 08 Dec 2021 22:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.05_summits.bed INFO @ Wed, 08 Dec 2021 22:44:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:44:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:44:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:44:47: #1 total tags in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:44:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:44:48: #1 tags after filtering in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:44:48: #1 finished! INFO @ Wed, 08 Dec 2021 22:44:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:44:48: #2 number of paired peaks: 483 WARNING @ Wed, 08 Dec 2021 22:44:48: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Wed, 08 Dec 2021 22:44:48: start model_add_line... INFO @ Wed, 08 Dec 2021 22:44:48: start X-correlation... INFO @ Wed, 08 Dec 2021 22:44:48: end of X-cor INFO @ Wed, 08 Dec 2021 22:44:48: #2 finished! INFO @ Wed, 08 Dec 2021 22:44:48: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:44:48: #2 alternative fragment length(s) may be 2,47,569 bps INFO @ Wed, 08 Dec 2021 22:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10_model.r WARNING @ Wed, 08 Dec 2021 22:44:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:44:48: #2 You may need to consider one of the other alternative d(s): 2,47,569 WARNING @ Wed, 08 Dec 2021 22:44:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:44:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:44:50: 7000000 INFO @ Wed, 08 Dec 2021 22:45:00: 8000000 INFO @ Wed, 08 Dec 2021 22:45:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:45:09: 9000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:45:20: 10000000 INFO @ Wed, 08 Dec 2021 22:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.10_summits.bed INFO @ Wed, 08 Dec 2021 22:45:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:45:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:45:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:45:26: #1 total tags in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:45:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:45:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:45:26: #1 tags after filtering in treatment: 10607018 INFO @ Wed, 08 Dec 2021 22:45:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:45:26: #1 finished! INFO @ Wed, 08 Dec 2021 22:45:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:45:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:45:27: #2 number of paired peaks: 483 WARNING @ Wed, 08 Dec 2021 22:45:27: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Wed, 08 Dec 2021 22:45:27: start model_add_line... INFO @ Wed, 08 Dec 2021 22:45:27: start X-correlation... INFO @ Wed, 08 Dec 2021 22:45:27: end of X-cor INFO @ Wed, 08 Dec 2021 22:45:27: #2 finished! INFO @ Wed, 08 Dec 2021 22:45:27: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:45:27: #2 alternative fragment length(s) may be 2,47,569 bps INFO @ Wed, 08 Dec 2021 22:45:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20_model.r WARNING @ Wed, 08 Dec 2021 22:45:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:45:27: #2 You may need to consider one of the other alternative d(s): 2,47,569 WARNING @ Wed, 08 Dec 2021 22:45:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:45:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:45:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:45:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180826/SRX3180826.20_summits.bed INFO @ Wed, 08 Dec 2021 22:46:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling