Job ID = 14160702 SRX = SRX10399015 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: 00:06:31 19274405 reads; of these: 19274405 (100.00%) were unpaired; of these: 5875257 (30.48%) aligned 0 times 11281907 (58.53%) aligned exactly 1 time 2117241 (10.98%) aligned >1 times 69.52% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 2819025 / 13399148 = 0.2104 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 03:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.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 03:59:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:55: 1000000 INFO @ Thu, 09 Dec 2021 04:00:05: 2000000 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 04:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.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 04:00:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:00:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:00:15: 3000000 INFO @ Thu, 09 Dec 2021 04:00:24: 1000000 INFO @ Thu, 09 Dec 2021 04:00:26: 4000000 INFO @ Thu, 09 Dec 2021 04:00:33: 2000000 INFO @ Thu, 09 Dec 2021 04:00:36: 5000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 04:00:42: 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 04:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.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 04:00:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:00:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:00:46: 6000000 INFO @ Thu, 09 Dec 2021 04:00:51: 4000000 INFO @ Thu, 09 Dec 2021 04:00:57: 7000000 INFO @ Thu, 09 Dec 2021 04:00:59: 1000000 INFO @ Thu, 09 Dec 2021 04:01:00: 5000000 INFO @ Thu, 09 Dec 2021 04:01:08: 8000000 INFO @ Thu, 09 Dec 2021 04:01:10: 6000000 INFO @ Thu, 09 Dec 2021 04:01:12: 2000000 INFO @ Thu, 09 Dec 2021 04:01:19: 9000000 INFO @ Thu, 09 Dec 2021 04:01:19: 7000000 INFO @ Thu, 09 Dec 2021 04:01:25: 3000000 INFO @ Thu, 09 Dec 2021 04:01:29: 8000000 INFO @ Thu, 09 Dec 2021 04:01:30: 10000000 INFO @ Thu, 09 Dec 2021 04:01:36: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:01:36: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:01:36: #1 total tags in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:01:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:01:36: #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 04:01:36: #1 tags after filtering in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:01:36: #1 finished! INFO @ Thu, 09 Dec 2021 04:01:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:01:37: #2 number of paired peaks: 537 WARNING @ Thu, 09 Dec 2021 04:01:37: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Thu, 09 Dec 2021 04:01:37: start model_add_line... INFO @ Thu, 09 Dec 2021 04:01:37: start X-correlation... INFO @ Thu, 09 Dec 2021 04:01:37: end of X-cor INFO @ Thu, 09 Dec 2021 04:01:37: #2 finished! INFO @ Thu, 09 Dec 2021 04:01:37: #2 predicted fragment length is 127 bps INFO @ Thu, 09 Dec 2021 04:01:37: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 09 Dec 2021 04:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05_model.r WARNING @ Thu, 09 Dec 2021 04:01:37: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:01:37: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 09 Dec 2021 04:01:37: #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 04:01:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:01:38: 9000000 INFO @ Thu, 09 Dec 2021 04:01:39: 4000000 INFO @ Thu, 09 Dec 2021 04:01:47: 10000000 INFO @ Thu, 09 Dec 2021 04:01:52: 5000000 INFO @ Thu, 09 Dec 2021 04:01:52: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:01:52: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:01:52: #1 total tags in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:01:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:01:52: #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 04:01:53: #1 tags after filtering in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:01:53: #1 finished! INFO @ Thu, 09 Dec 2021 04:01:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:01:54: #2 number of paired peaks: 537 WARNING @ Thu, 09 Dec 2021 04:01:54: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Thu, 09 Dec 2021 04:01:54: start model_add_line... INFO @ Thu, 09 Dec 2021 04:01:54: start X-correlation... INFO @ Thu, 09 Dec 2021 04:01:54: end of X-cor INFO @ Thu, 09 Dec 2021 04:01:54: #2 finished! INFO @ Thu, 09 Dec 2021 04:01:54: #2 predicted fragment length is 127 bps INFO @ Thu, 09 Dec 2021 04:01:54: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 09 Dec 2021 04:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10_model.r WARNING @ Thu, 09 Dec 2021 04:01:54: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:01:54: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 09 Dec 2021 04:01:54: #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 04:01:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:01:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:02:06: 6000000 INFO @ Thu, 09 Dec 2021 04:02:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:02:21: 7000000 INFO @ Thu, 09 Dec 2021 04:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.05_summits.bed INFO @ Thu, 09 Dec 2021 04:02:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1768 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:02:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:02:35: 8000000 INFO @ Thu, 09 Dec 2021 04:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.10_summits.bed INFO @ Thu, 09 Dec 2021 04:02:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1149 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:02:47: 9000000 INFO @ Thu, 09 Dec 2021 04:02:59: 10000000 INFO @ Thu, 09 Dec 2021 04:03:06: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:03:06: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:03:06: #1 total tags in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:03:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:06: #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 04:03:07: #1 tags after filtering in treatment: 10580123 INFO @ Thu, 09 Dec 2021 04:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:03:07: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:07: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:08: #2 number of paired peaks: 537 WARNING @ Thu, 09 Dec 2021 04:03:08: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:08: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:08: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:08: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:08: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:08: #2 predicted fragment length is 127 bps INFO @ Thu, 09 Dec 2021 04:03:08: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 09 Dec 2021 04:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20_model.r WARNING @ Thu, 09 Dec 2021 04:03:08: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:03:08: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 09 Dec 2021 04:03:08: #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 04:03:08: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399015/SRX10399015.20_summits.bed INFO @ Thu, 09 Dec 2021 04:03:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 3 millis CompletedMACS2peakCalling