Job ID = 14159589 SRX = SRX3180776 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18134381 spots for SRR6030427/SRR6030427.sra Written 18134381 spots for SRR6030427/SRR6030427.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159951 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:46 18134381 reads; of these: 18134381 (100.00%) were unpaired; of these: 704870 (3.89%) aligned 0 times 14514570 (80.04%) aligned exactly 1 time 2914941 (16.07%) aligned >1 times 96.11% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 3350184 / 17429511 = 0.1922 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 23:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.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 23:10:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:10:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:10:31: 1000000 INFO @ Wed, 08 Dec 2021 23:10:39: 2000000 INFO @ Wed, 08 Dec 2021 23:10:47: 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 23:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.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 23:10:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:10:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:10:55: 4000000 INFO @ Wed, 08 Dec 2021 23:11:00: 1000000 INFO @ Wed, 08 Dec 2021 23:11:03: 5000000 INFO @ Wed, 08 Dec 2021 23:11:09: 2000000 INFO @ Wed, 08 Dec 2021 23:11:11: 6000000 INFO @ Wed, 08 Dec 2021 23:11:17: 3000000 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 23:11:20: 7000000 INFO @ Wed, 08 Dec 2021 23:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.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 23:11:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:11:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:11:26: 4000000 INFO @ Wed, 08 Dec 2021 23:11:28: 8000000 INFO @ Wed, 08 Dec 2021 23:11:29: 1000000 INFO @ Wed, 08 Dec 2021 23:11:34: 5000000 INFO @ Wed, 08 Dec 2021 23:11:35: 9000000 INFO @ Wed, 08 Dec 2021 23:11:38: 2000000 INFO @ Wed, 08 Dec 2021 23:11:42: 6000000 INFO @ Wed, 08 Dec 2021 23:11:44: 10000000 INFO @ Wed, 08 Dec 2021 23:11:46: 3000000 INFO @ Wed, 08 Dec 2021 23:11:50: 7000000 INFO @ Wed, 08 Dec 2021 23:11:51: 11000000 INFO @ Wed, 08 Dec 2021 23:11:54: 4000000 INFO @ Wed, 08 Dec 2021 23:11:58: 8000000 INFO @ Wed, 08 Dec 2021 23:12:00: 12000000 INFO @ Wed, 08 Dec 2021 23:12:03: 5000000 INFO @ Wed, 08 Dec 2021 23:12:06: 9000000 INFO @ Wed, 08 Dec 2021 23:12:08: 13000000 INFO @ Wed, 08 Dec 2021 23:12:11: 6000000 INFO @ Wed, 08 Dec 2021 23:12:15: 10000000 INFO @ Wed, 08 Dec 2021 23:12:16: 14000000 INFO @ Wed, 08 Dec 2021 23:12:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:12:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:12:17: #1 total tags in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:12:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:12:17: #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 23:12:17: #1 tags after filtering in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:12:17: #1 finished! INFO @ Wed, 08 Dec 2021 23:12:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:12:18: #2 number of paired peaks: 315 WARNING @ Wed, 08 Dec 2021 23:12:18: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 08 Dec 2021 23:12:18: start model_add_line... INFO @ Wed, 08 Dec 2021 23:12:18: start X-correlation... INFO @ Wed, 08 Dec 2021 23:12:18: end of X-cor INFO @ Wed, 08 Dec 2021 23:12:18: #2 finished! INFO @ Wed, 08 Dec 2021 23:12:18: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 23:12:18: #2 alternative fragment length(s) may be 2,44,560 bps INFO @ Wed, 08 Dec 2021 23:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05_model.r WARNING @ Wed, 08 Dec 2021 23:12:18: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:12:18: #2 You may need to consider one of the other alternative d(s): 2,44,560 WARNING @ Wed, 08 Dec 2021 23:12:18: #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 23:12:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:12:19: 7000000 INFO @ Wed, 08 Dec 2021 23:12:23: 11000000 INFO @ Wed, 08 Dec 2021 23:12:28: 8000000 INFO @ Wed, 08 Dec 2021 23:12:31: 12000000 INFO @ Wed, 08 Dec 2021 23:12:36: 9000000 INFO @ Wed, 08 Dec 2021 23:12:40: 13000000 INFO @ Wed, 08 Dec 2021 23:12:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:12:44: 10000000 INFO @ Wed, 08 Dec 2021 23:12:48: 14000000 INFO @ Wed, 08 Dec 2021 23:12:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:12:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:12:48: #1 total tags in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:12:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:12:48: #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 23:12:49: #1 tags after filtering in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:12:49: #1 finished! INFO @ Wed, 08 Dec 2021 23:12:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:12:50: #2 number of paired peaks: 315 WARNING @ Wed, 08 Dec 2021 23:12:50: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 08 Dec 2021 23:12:50: start model_add_line... INFO @ Wed, 08 Dec 2021 23:12:50: start X-correlation... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:12:50: end of X-cor INFO @ Wed, 08 Dec 2021 23:12:50: #2 finished! INFO @ Wed, 08 Dec 2021 23:12:50: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 23:12:50: #2 alternative fragment length(s) may be 2,44,560 bps INFO @ Wed, 08 Dec 2021 23:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10_model.r WARNING @ Wed, 08 Dec 2021 23:12:50: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:12:50: #2 You may need to consider one of the other alternative d(s): 2,44,560 WARNING @ Wed, 08 Dec 2021 23:12:50: #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 23:12:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:12:52: 11000000 INFO @ Wed, 08 Dec 2021 23:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.05_summits.bed INFO @ Wed, 08 Dec 2021 23:12:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (699 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:13:01: 12000000 INFO @ Wed, 08 Dec 2021 23:13:09: 13000000 INFO @ Wed, 08 Dec 2021 23:13:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:13:16: 14000000 INFO @ Wed, 08 Dec 2021 23:13:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:13:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:13:17: #1 total tags in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:13:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:13:17: #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 23:13:17: #1 tags after filtering in treatment: 14079327 INFO @ Wed, 08 Dec 2021 23:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:13:17: #1 finished! INFO @ Wed, 08 Dec 2021 23:13:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:13:18: #2 number of paired peaks: 315 WARNING @ Wed, 08 Dec 2021 23:13:18: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 08 Dec 2021 23:13:18: start model_add_line... INFO @ Wed, 08 Dec 2021 23:13:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:13:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:13:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:13:19: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 23:13:19: #2 alternative fragment length(s) may be 2,44,560 bps INFO @ Wed, 08 Dec 2021 23:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20_model.r WARNING @ Wed, 08 Dec 2021 23:13:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:13:19: #2 You may need to consider one of the other alternative d(s): 2,44,560 WARNING @ Wed, 08 Dec 2021 23:13:19: #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 23:13:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.10_summits.bed INFO @ Wed, 08 Dec 2021 23:13:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:13:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180776/SRX3180776.20_summits.bed INFO @ Wed, 08 Dec 2021 23:13:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling