Job ID = 14160766 SRX = SRX10399037 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: 00:05:55 18655141 reads; of these: 18655141 (100.00%) were unpaired; of these: 1684555 (9.03%) aligned 0 times 14079577 (75.47%) aligned exactly 1 time 2891009 (15.50%) aligned >1 times 90.97% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 2044077 / 16970586 = 0.1204 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 04:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.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 04:16:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:16:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:16:42: 1000000 INFO @ Thu, 09 Dec 2021 04:16:49: 2000000 INFO @ Thu, 09 Dec 2021 04:16:57: 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 04:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.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 04:17:04: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:17:04: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:17:05: 4000000 INFO @ Thu, 09 Dec 2021 04:17:13: 1000000 INFO @ Thu, 09 Dec 2021 04:17:13: 5000000 INFO @ Thu, 09 Dec 2021 04:17:21: 2000000 INFO @ Thu, 09 Dec 2021 04:17:22: 6000000 INFO @ Thu, 09 Dec 2021 04:17:30: 3000000 INFO @ Thu, 09 Dec 2021 04:17:30: 7000000 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 04:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.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 04:17:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:17:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:17:38: 4000000 INFO @ Thu, 09 Dec 2021 04:17:38: 8000000 INFO @ Thu, 09 Dec 2021 04:17:42: 1000000 INFO @ Thu, 09 Dec 2021 04:17:47: 5000000 INFO @ Thu, 09 Dec 2021 04:17:47: 9000000 INFO @ Thu, 09 Dec 2021 04:17:49: 2000000 INFO @ Thu, 09 Dec 2021 04:17:55: 6000000 INFO @ Thu, 09 Dec 2021 04:17:55: 10000000 INFO @ Thu, 09 Dec 2021 04:17:57: 3000000 INFO @ Thu, 09 Dec 2021 04:18:03: 11000000 INFO @ Thu, 09 Dec 2021 04:18:03: 7000000 INFO @ Thu, 09 Dec 2021 04:18:04: 4000000 INFO @ Thu, 09 Dec 2021 04:18:11: 12000000 INFO @ Thu, 09 Dec 2021 04:18:12: 8000000 INFO @ Thu, 09 Dec 2021 04:18:12: 5000000 INFO @ Thu, 09 Dec 2021 04:18:20: 6000000 INFO @ Thu, 09 Dec 2021 04:18:20: 13000000 INFO @ Thu, 09 Dec 2021 04:18:20: 9000000 INFO @ Thu, 09 Dec 2021 04:18:27: 7000000 INFO @ Thu, 09 Dec 2021 04:18:28: 14000000 INFO @ Thu, 09 Dec 2021 04:18:28: 10000000 INFO @ Thu, 09 Dec 2021 04:18:35: 8000000 INFO @ Thu, 09 Dec 2021 04:18:36: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:18:36: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:18:36: #1 total tags in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:18:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:18:36: #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 04:18:36: #1 tags after filtering in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:18:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:18:36: #1 finished! INFO @ Thu, 09 Dec 2021 04:18:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:18:37: 11000000 INFO @ Thu, 09 Dec 2021 04:18:37: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 04:18:37: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 04:18:37: start model_add_line... INFO @ Thu, 09 Dec 2021 04:18:37: start X-correlation... INFO @ Thu, 09 Dec 2021 04:18:37: end of X-cor INFO @ Thu, 09 Dec 2021 04:18:37: #2 finished! INFO @ Thu, 09 Dec 2021 04:18:37: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:18:37: #2 alternative fragment length(s) may be 2,65 bps INFO @ Thu, 09 Dec 2021 04:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05_model.r WARNING @ Thu, 09 Dec 2021 04:18:37: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:18:37: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Thu, 09 Dec 2021 04:18:37: #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 04:18:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:18:42: 9000000 INFO @ Thu, 09 Dec 2021 04:18:45: 12000000 INFO @ Thu, 09 Dec 2021 04:18:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:18:53: 13000000 INFO @ Thu, 09 Dec 2021 04:18:57: 11000000 INFO @ Thu, 09 Dec 2021 04:19:01: 14000000 INFO @ Thu, 09 Dec 2021 04:19:04: 12000000 INFO @ Thu, 09 Dec 2021 04:19:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:19:09: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:19:09: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:19:09: #1 total tags in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:19:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:19:09: #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 04:19:09: #1 tags after filtering in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:19:09: #1 finished! INFO @ Thu, 09 Dec 2021 04:19:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:19:10: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 04:19:10: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 04:19:10: start model_add_line... INFO @ Thu, 09 Dec 2021 04:19:10: start X-correlation... INFO @ Thu, 09 Dec 2021 04:19:10: end of X-cor INFO @ Thu, 09 Dec 2021 04:19:10: #2 finished! INFO @ Thu, 09 Dec 2021 04:19:10: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:19:10: #2 alternative fragment length(s) may be 2,65 bps INFO @ Thu, 09 Dec 2021 04:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10_model.r WARNING @ Thu, 09 Dec 2021 04:19:10: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:19:10: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Thu, 09 Dec 2021 04:19:10: #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 04:19:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:19:11: 13000000 INFO @ Thu, 09 Dec 2021 04:19:17: 14000000 INFO @ Thu, 09 Dec 2021 04:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.05_summits.bed INFO @ Thu, 09 Dec 2021 04:19:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (901 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:19:23: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 04:19:23: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 04:19:23: #1 total tags in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:19:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:19:23: #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 04:19:23: #1 tags after filtering in treatment: 14926509 INFO @ Thu, 09 Dec 2021 04:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:19:23: #1 finished! INFO @ Thu, 09 Dec 2021 04:19:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:19:24: #2 number of paired peaks: 266 WARNING @ Thu, 09 Dec 2021 04:19:24: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Thu, 09 Dec 2021 04:19:24: start model_add_line... INFO @ Thu, 09 Dec 2021 04:19:25: start X-correlation... INFO @ Thu, 09 Dec 2021 04:19:25: end of X-cor INFO @ Thu, 09 Dec 2021 04:19:25: #2 finished! INFO @ Thu, 09 Dec 2021 04:19:25: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:19:25: #2 alternative fragment length(s) may be 2,65 bps INFO @ Thu, 09 Dec 2021 04:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20_model.r WARNING @ Thu, 09 Dec 2021 04:19:25: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:19:25: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Thu, 09 Dec 2021 04:19:25: #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 04:19:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:19:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:19:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.10_summits.bed INFO @ Thu, 09 Dec 2021 04:19:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:19:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399037/SRX10399037.20_summits.bed INFO @ Thu, 09 Dec 2021 04:20:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 1 millis CompletedMACS2peakCalling