Job ID = 14160125 SRX = SRX3180785 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: 00:03:54 11621086 reads; of these: 11621086 (100.00%) were unpaired; of these: 451857 (3.89%) aligned 0 times 9033630 (77.73%) aligned exactly 1 time 2135599 (18.38%) aligned >1 times 96.11% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1216384 / 11169229 = 0.1089 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 01:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.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 01:01:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:01:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:01:44: 1000000 INFO @ Thu, 09 Dec 2021 01:01:52: 2000000 INFO @ Thu, 09 Dec 2021 01:02:01: 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 01:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.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 01:02:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:02:06: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:02:10: 4000000 INFO @ Thu, 09 Dec 2021 01:02:15: 1000000 INFO @ Thu, 09 Dec 2021 01:02:19: 5000000 INFO @ Thu, 09 Dec 2021 01:02:24: 2000000 INFO @ Thu, 09 Dec 2021 01:02:28: 6000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 01:02:33: 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 01:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.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 01:02:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:02:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:02:37: 7000000 INFO @ Thu, 09 Dec 2021 01:02:42: 4000000 INFO @ Thu, 09 Dec 2021 01:02:46: 1000000 INFO @ Thu, 09 Dec 2021 01:02:46: 8000000 INFO @ Thu, 09 Dec 2021 01:02:51: 5000000 INFO @ Thu, 09 Dec 2021 01:02:55: 2000000 INFO @ Thu, 09 Dec 2021 01:02:57: 9000000 INFO @ Thu, 09 Dec 2021 01:03:00: 6000000 INFO @ Thu, 09 Dec 2021 01:03:04: 3000000 INFO @ Thu, 09 Dec 2021 01:03:06: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:03:06: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:03:06: #1 total tags in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:03:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:03:06: #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 01:03:06: #1 tags after filtering in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:03:06: #1 finished! INFO @ Thu, 09 Dec 2021 01:03:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:03:07: #2 number of paired peaks: 395 WARNING @ Thu, 09 Dec 2021 01:03:07: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Thu, 09 Dec 2021 01:03:07: start model_add_line... INFO @ Thu, 09 Dec 2021 01:03:07: start X-correlation... INFO @ Thu, 09 Dec 2021 01:03:07: end of X-cor INFO @ Thu, 09 Dec 2021 01:03:07: #2 finished! INFO @ Thu, 09 Dec 2021 01:03:07: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:03:07: #2 alternative fragment length(s) may be 3,48,564,566 bps INFO @ Thu, 09 Dec 2021 01:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05_model.r WARNING @ Thu, 09 Dec 2021 01:03:07: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:03:07: #2 You may need to consider one of the other alternative d(s): 3,48,564,566 WARNING @ Thu, 09 Dec 2021 01:03:07: #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 01:03:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:03:09: 7000000 INFO @ Thu, 09 Dec 2021 01:03:12: 4000000 INFO @ Thu, 09 Dec 2021 01:03:17: 8000000 INFO @ Thu, 09 Dec 2021 01:03:21: 5000000 INFO @ Thu, 09 Dec 2021 01:03:26: 9000000 INFO @ Thu, 09 Dec 2021 01:03:29: 6000000 INFO @ Thu, 09 Dec 2021 01:03:34: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:03:34: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:03:34: #1 total tags in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:03:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:03:34: #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 01:03:35: #1 tags after filtering in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:03:35: #1 finished! INFO @ Thu, 09 Dec 2021 01:03:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:03:36: #2 number of paired peaks: 395 WARNING @ Thu, 09 Dec 2021 01:03:36: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Thu, 09 Dec 2021 01:03:36: start model_add_line... INFO @ Thu, 09 Dec 2021 01:03:36: start X-correlation... INFO @ Thu, 09 Dec 2021 01:03:36: end of X-cor INFO @ Thu, 09 Dec 2021 01:03:36: #2 finished! INFO @ Thu, 09 Dec 2021 01:03:36: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:03:36: #2 alternative fragment length(s) may be 3,48,564,566 bps INFO @ Thu, 09 Dec 2021 01:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10_model.r WARNING @ Thu, 09 Dec 2021 01:03:36: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:03:36: #2 You may need to consider one of the other alternative d(s): 3,48,564,566 WARNING @ Thu, 09 Dec 2021 01:03:36: #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 01:03:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:03:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:03:38: 7000000 INFO @ Thu, 09 Dec 2021 01:03:46: 8000000 INFO @ Thu, 09 Dec 2021 01:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.05_summits.bed INFO @ Thu, 09 Dec 2021 01:03:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:03:54: 9000000 INFO @ Thu, 09 Dec 2021 01:04:02: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:04:02: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:04:02: #1 total tags in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:04:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:04:02: #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 01:04:02: #1 tags after filtering in treatment: 9952845 INFO @ Thu, 09 Dec 2021 01:04:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:04:02: #1 finished! INFO @ Thu, 09 Dec 2021 01:04:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:04:03: #2 number of paired peaks: 395 WARNING @ Thu, 09 Dec 2021 01:04:03: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Thu, 09 Dec 2021 01:04:03: start model_add_line... INFO @ Thu, 09 Dec 2021 01:04:03: start X-correlation... INFO @ Thu, 09 Dec 2021 01:04:03: end of X-cor INFO @ Thu, 09 Dec 2021 01:04:03: #2 finished! INFO @ Thu, 09 Dec 2021 01:04:03: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:04:03: #2 alternative fragment length(s) may be 3,48,564,566 bps INFO @ Thu, 09 Dec 2021 01:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20_model.r WARNING @ Thu, 09 Dec 2021 01:04:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:04:03: #2 You may need to consider one of the other alternative d(s): 3,48,564,566 WARNING @ Thu, 09 Dec 2021 01:04:03: #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 01:04:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:04:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.10_summits.bed INFO @ Thu, 09 Dec 2021 01:04:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:04:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180785/SRX3180785.20_summits.bed INFO @ Thu, 09 Dec 2021 01:04:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 5 millis CompletedMACS2peakCalling