Job ID = 14160547 SRX = SRX10399004 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12830116 spots for SRR14022429/SRR14022429.sra Written 12830116 spots for SRR14022429/SRR14022429.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160680 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:08 12830116 reads; of these: 12830116 (100.00%) were unpaired; of these: 826551 (6.44%) aligned 0 times 9991414 (77.87%) aligned exactly 1 time 2012151 (15.68%) aligned >1 times 93.56% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 1207210 / 12003565 = 0.1006 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 03:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.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 03:16:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:16:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:16:51: 1000000 INFO @ Thu, 09 Dec 2021 03:16:56: 2000000 INFO @ Thu, 09 Dec 2021 03:17:01: 3000000 INFO @ Thu, 09 Dec 2021 03:17:07: 4000000 INFO @ Thu, 09 Dec 2021 03:17:12: 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 @ Thu, 09 Dec 2021 03:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.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 03:17:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:18: 6000000 INFO @ Thu, 09 Dec 2021 03:17:22: 1000000 INFO @ Thu, 09 Dec 2021 03:17:23: 7000000 INFO @ Thu, 09 Dec 2021 03:17:28: 2000000 INFO @ Thu, 09 Dec 2021 03:17:29: 8000000 INFO @ Thu, 09 Dec 2021 03:17:35: 9000000 INFO @ Thu, 09 Dec 2021 03:17:35: 3000000 INFO @ Thu, 09 Dec 2021 03:17:40: 10000000 INFO @ Thu, 09 Dec 2021 03:17:41: 4000000 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 @ Thu, 09 Dec 2021 03:17:45: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:17:45: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:17:45: #1 total tags in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:17:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:45: #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 03:17:45: #1 tags after filtering in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:17:45: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.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 03:17:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:46: #2 number of paired peaks: 321 WARNING @ Thu, 09 Dec 2021 03:17:46: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:46: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:46: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:46: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:46: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:46: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:17:46: #2 alternative fragment length(s) may be 4,74,575 bps INFO @ Thu, 09 Dec 2021 03:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05_model.r WARNING @ Thu, 09 Dec 2021 03:17:46: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:17:46: #2 You may need to consider one of the other alternative d(s): 4,74,575 WARNING @ Thu, 09 Dec 2021 03:17:46: #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 03:17:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:48: 5000000 INFO @ Thu, 09 Dec 2021 03:17:51: 1000000 INFO @ Thu, 09 Dec 2021 03:17:54: 6000000 INFO @ Thu, 09 Dec 2021 03:17:57: 2000000 INFO @ Thu, 09 Dec 2021 03:18:01: 7000000 INFO @ Thu, 09 Dec 2021 03:18:03: 3000000 INFO @ Thu, 09 Dec 2021 03:18:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:07: 8000000 INFO @ Thu, 09 Dec 2021 03:18:08: 4000000 INFO @ Thu, 09 Dec 2021 03:18:14: 9000000 INFO @ Thu, 09 Dec 2021 03:18:14: 5000000 INFO @ Thu, 09 Dec 2021 03:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.05_summits.bed INFO @ Thu, 09 Dec 2021 03:18:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:18:20: 6000000 INFO @ Thu, 09 Dec 2021 03:18:20: 10000000 INFO @ Thu, 09 Dec 2021 03:18:25: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:18:25: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:18:25: #1 total tags in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:18:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:25: #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 03:18:25: #1 tags after filtering in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:18:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:18:25: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:26: 7000000 INFO @ Thu, 09 Dec 2021 03:18:26: #2 number of paired peaks: 321 WARNING @ Thu, 09 Dec 2021 03:18:26: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:26: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:26: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:26: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:26: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:26: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:18:26: #2 alternative fragment length(s) may be 4,74,575 bps INFO @ Thu, 09 Dec 2021 03:18:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10_model.r WARNING @ Thu, 09 Dec 2021 03:18:26: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:18:26: #2 You may need to consider one of the other alternative d(s): 4,74,575 WARNING @ Thu, 09 Dec 2021 03:18:26: #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 03:18:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:18:36: 9000000 INFO @ Thu, 09 Dec 2021 03:18:42: 10000000 INFO @ Thu, 09 Dec 2021 03:18:46: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:18:46: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:18:46: #1 total tags in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:18:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:46: #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 03:18:46: #1 tags after filtering in treatment: 10796355 INFO @ Thu, 09 Dec 2021 03:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:18:46: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:47: #2 number of paired peaks: 321 WARNING @ Thu, 09 Dec 2021 03:18:47: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:47: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:47: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:47: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:47: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:47: #2 predicted fragment length is 74 bps INFO @ Thu, 09 Dec 2021 03:18:47: #2 alternative fragment length(s) may be 4,74,575 bps INFO @ Thu, 09 Dec 2021 03:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20_model.r WARNING @ Thu, 09 Dec 2021 03:18:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:18:47: #2 You may need to consider one of the other alternative d(s): 4,74,575 WARNING @ Thu, 09 Dec 2021 03:18:47: #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 03:18:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.10_summits.bed INFO @ Thu, 09 Dec 2021 03:18:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:19:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399004/SRX10399004.20_summits.bed INFO @ Thu, 09 Dec 2021 03:19:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling