Job ID = 14159482 SRX = SRX3180810 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: 00:03:26 17572071 reads; of these: 17572071 (100.00%) were unpaired; of these: 1363955 (7.76%) aligned 0 times 13321442 (75.81%) aligned exactly 1 time 2886674 (16.43%) aligned >1 times 92.24% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 4869649 / 16208116 = 0.3004 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 22:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.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 22:14:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:14:12: 1000000 INFO @ Wed, 08 Dec 2021 22:14:17: 2000000 INFO @ Wed, 08 Dec 2021 22:14:23: 3000000 INFO @ Wed, 08 Dec 2021 22:14:28: 4000000 INFO @ Wed, 08 Dec 2021 22:14:33: 5000000 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 22:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.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 22:14:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:14:39: 6000000 INFO @ Wed, 08 Dec 2021 22:14:41: 1000000 INFO @ Wed, 08 Dec 2021 22:14:44: 7000000 INFO @ Wed, 08 Dec 2021 22:14:46: 2000000 INFO @ Wed, 08 Dec 2021 22:14:49: 8000000 INFO @ Wed, 08 Dec 2021 22:14:50: 3000000 INFO @ Wed, 08 Dec 2021 22:14:55: 9000000 INFO @ Wed, 08 Dec 2021 22:14:55: 4000000 INFO @ Wed, 08 Dec 2021 22:15:00: 5000000 INFO @ Wed, 08 Dec 2021 22:15:00: 10000000 INFO @ Wed, 08 Dec 2021 22:15:04: 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 22:15:05: 11000000 INFO @ Wed, 08 Dec 2021 22:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.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 22:15:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:07: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:15:07: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:15:07: #1 total tags in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:15:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:07: #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 22:15:08: #1 tags after filtering in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:15:08: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:08: #2 number of paired peaks: 417 WARNING @ Wed, 08 Dec 2021 22:15:08: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 08 Dec 2021 22:15:08: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:08: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:08: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:08: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:08: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:15:08: #2 alternative fragment length(s) may be 1,47,542,563,567 bps INFO @ Wed, 08 Dec 2021 22:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05_model.r WARNING @ Wed, 08 Dec 2021 22:15:08: #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 22:15:08: #2 You may need to consider one of the other alternative d(s): 1,47,542,563,567 WARNING @ Wed, 08 Dec 2021 22:15:08: #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 22:15:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:09: 7000000 INFO @ Wed, 08 Dec 2021 22:15:12: 1000000 INFO @ Wed, 08 Dec 2021 22:15:13: 8000000 INFO @ Wed, 08 Dec 2021 22:15:17: 2000000 INFO @ Wed, 08 Dec 2021 22:15:18: 9000000 INFO @ Wed, 08 Dec 2021 22:15:23: 10000000 INFO @ Wed, 08 Dec 2021 22:15:23: 3000000 INFO @ Wed, 08 Dec 2021 22:15:27: 11000000 INFO @ Wed, 08 Dec 2021 22:15:28: 4000000 INFO @ Wed, 08 Dec 2021 22:15:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:15:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:15:29: #1 total tags in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:15:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:29: #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 22:15:29: #1 tags after filtering in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:15:29: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:30: #2 number of paired peaks: 417 WARNING @ Wed, 08 Dec 2021 22:15:30: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 08 Dec 2021 22:15:30: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:30: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:30: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:30: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:30: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:15:30: #2 alternative fragment length(s) may be 1,47,542,563,567 bps INFO @ Wed, 08 Dec 2021 22:15:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10_model.r WARNING @ Wed, 08 Dec 2021 22:15:30: #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 22:15:30: #2 You may need to consider one of the other alternative d(s): 1,47,542,563,567 WARNING @ Wed, 08 Dec 2021 22:15:30: #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 22:15:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:33: 5000000 INFO @ Wed, 08 Dec 2021 22:15:39: 6000000 INFO @ Wed, 08 Dec 2021 22:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.05_summits.bed INFO @ Wed, 08 Dec 2021 22:15:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (722 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:15:44: 7000000 INFO @ Wed, 08 Dec 2021 22:15:49: 8000000 INFO @ Wed, 08 Dec 2021 22:15:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:55: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:16:00: 10000000 INFO @ Wed, 08 Dec 2021 22:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.10_summits.bed INFO @ Wed, 08 Dec 2021 22:16:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:16:05: 11000000 INFO @ Wed, 08 Dec 2021 22:16:07: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:16:07: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:16:07: #1 total tags in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:16:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:07: #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 22:16:07: #1 tags after filtering in treatment: 11338467 INFO @ Wed, 08 Dec 2021 22:16:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:16:07: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:16:08: #2 number of paired peaks: 417 WARNING @ Wed, 08 Dec 2021 22:16:08: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Wed, 08 Dec 2021 22:16:08: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:08: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:08: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:08: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:08: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 22:16:08: #2 alternative fragment length(s) may be 1,47,542,563,567 bps INFO @ Wed, 08 Dec 2021 22:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20_model.r WARNING @ Wed, 08 Dec 2021 22:16:08: #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 22:16:08: #2 You may need to consider one of the other alternative d(s): 1,47,542,563,567 WARNING @ Wed, 08 Dec 2021 22:16:08: #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 22:16:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:16:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180810/SRX3180810.20_summits.bed INFO @ Wed, 08 Dec 2021 22:16:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling