Job ID = 14158929 SRX = SRX7665451 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: 00:05:09 31920556 reads; of these: 31920556 (100.00%) were unpaired; of these: 2296932 (7.20%) aligned 0 times 25068753 (78.53%) aligned exactly 1 time 4554871 (14.27%) aligned >1 times 92.80% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 22229101 / 29623624 = 0.7504 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 18:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.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 18:32:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:32:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:32:45: 1000000 INFO @ Wed, 08 Dec 2021 18:32:49: 2000000 INFO @ Wed, 08 Dec 2021 18:32:54: 3000000 INFO @ Wed, 08 Dec 2021 18:32:58: 4000000 INFO @ Wed, 08 Dec 2021 18:33:03: 5000000 INFO @ Wed, 08 Dec 2021 18:33:08: 6000000 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 18:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.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 18:33:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:33:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:33:12: 7000000 INFO @ Wed, 08 Dec 2021 18:33:14: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:33:14: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:33:14: #1 total tags in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:33:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:33:14: #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 18:33:14: #1 tags after filtering in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:33:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:33:14: #1 finished! INFO @ Wed, 08 Dec 2021 18:33:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:33:15: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 18:33:15: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 18:33:15: start model_add_line... INFO @ Wed, 08 Dec 2021 18:33:15: start X-correlation... INFO @ Wed, 08 Dec 2021 18:33:15: end of X-cor INFO @ Wed, 08 Dec 2021 18:33:15: #2 finished! INFO @ Wed, 08 Dec 2021 18:33:15: #2 predicted fragment length is 38 bps INFO @ Wed, 08 Dec 2021 18:33:15: #2 alternative fragment length(s) may be 1,38,68 bps INFO @ Wed, 08 Dec 2021 18:33:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05_model.r INFO @ Wed, 08 Dec 2021 18:33:15: 1000000 WARNING @ Wed, 08 Dec 2021 18:33:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:33:15: #2 You may need to consider one of the other alternative d(s): 1,38,68 WARNING @ Wed, 08 Dec 2021 18:33:15: #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 18:33:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:33:19: 2000000 INFO @ Wed, 08 Dec 2021 18:33:24: 3000000 INFO @ Wed, 08 Dec 2021 18:33:29: 4000000 INFO @ Wed, 08 Dec 2021 18:33:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:33:33: 5000000 INFO @ Wed, 08 Dec 2021 18:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.05_summits.bed INFO @ Wed, 08 Dec 2021 18:33:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1433 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:33:38: 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 18:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.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 18:33:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:33:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:33:42: 7000000 INFO @ Wed, 08 Dec 2021 18:33:44: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:33:44: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:33:44: #1 total tags in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:33:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:33:44: #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 18:33:44: #1 tags after filtering in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:33:44: #1 finished! INFO @ Wed, 08 Dec 2021 18:33:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:33:45: 1000000 INFO @ Wed, 08 Dec 2021 18:33:45: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 18:33:45: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 18:33:45: start model_add_line... INFO @ Wed, 08 Dec 2021 18:33:45: start X-correlation... INFO @ Wed, 08 Dec 2021 18:33:45: end of X-cor INFO @ Wed, 08 Dec 2021 18:33:45: #2 finished! INFO @ Wed, 08 Dec 2021 18:33:45: #2 predicted fragment length is 38 bps INFO @ Wed, 08 Dec 2021 18:33:45: #2 alternative fragment length(s) may be 1,38,68 bps INFO @ Wed, 08 Dec 2021 18:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10_model.r WARNING @ Wed, 08 Dec 2021 18:33:45: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:33:45: #2 You may need to consider one of the other alternative d(s): 1,38,68 WARNING @ Wed, 08 Dec 2021 18:33:45: #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 18:33:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:33:49: 2000000 INFO @ Wed, 08 Dec 2021 18:33:54: 3000000 INFO @ Wed, 08 Dec 2021 18:33:59: 4000000 INFO @ Wed, 08 Dec 2021 18:33:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:34:03: 5000000 INFO @ Wed, 08 Dec 2021 18:34:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:34:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:34:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.10_summits.bed INFO @ Wed, 08 Dec 2021 18:34:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:34:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:34:12: 7000000 INFO @ Wed, 08 Dec 2021 18:34:14: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:34:14: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:34:14: #1 total tags in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:34:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:34:14: #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 18:34:14: #1 tags after filtering in treatment: 7394523 INFO @ Wed, 08 Dec 2021 18:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:34:14: #1 finished! INFO @ Wed, 08 Dec 2021 18:34:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:34:15: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 18:34:15: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 18:34:15: start model_add_line... INFO @ Wed, 08 Dec 2021 18:34:15: start X-correlation... INFO @ Wed, 08 Dec 2021 18:34:15: end of X-cor INFO @ Wed, 08 Dec 2021 18:34:15: #2 finished! INFO @ Wed, 08 Dec 2021 18:34:15: #2 predicted fragment length is 38 bps INFO @ Wed, 08 Dec 2021 18:34:15: #2 alternative fragment length(s) may be 1,38,68 bps INFO @ Wed, 08 Dec 2021 18:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20_model.r WARNING @ Wed, 08 Dec 2021 18:34:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:34:15: #2 You may need to consider one of the other alternative d(s): 1,38,68 WARNING @ Wed, 08 Dec 2021 18:34:15: #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 18:34:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:34:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:34:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665451/SRX7665451.20_summits.bed INFO @ Wed, 08 Dec 2021 18:34:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling