Job ID = 14160301 SRX = SRX8832063 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: 00:06:53 32508562 reads; of these: 32508562 (100.00%) were unpaired; of these: 492485 (1.51%) aligned 0 times 27114987 (83.41%) aligned exactly 1 time 4901090 (15.08%) aligned >1 times 98.49% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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 16 files... [bam_rmdupse_core] 9733030 / 32016077 = 0.3040 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 01:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.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 01:31:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:31:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:31:43: 1000000 INFO @ Thu, 09 Dec 2021 01:31:49: 2000000 INFO @ Thu, 09 Dec 2021 01:31:55: 3000000 INFO @ Thu, 09 Dec 2021 01:32:00: 4000000 INFO @ Thu, 09 Dec 2021 01:32:06: 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 01:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.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 01:32:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:32:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:32:11: 6000000 INFO @ Thu, 09 Dec 2021 01:32:13: 1000000 INFO @ Thu, 09 Dec 2021 01:32:17: 7000000 INFO @ Thu, 09 Dec 2021 01:32:18: 2000000 INFO @ Thu, 09 Dec 2021 01:32:23: 8000000 INFO @ Thu, 09 Dec 2021 01:32:23: 3000000 INFO @ Thu, 09 Dec 2021 01:32:28: 4000000 INFO @ Thu, 09 Dec 2021 01:32:29: 9000000 INFO @ Thu, 09 Dec 2021 01:32:33: 5000000 INFO @ Thu, 09 Dec 2021 01:32:34: 10000000 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 01:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.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 01:32:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:32:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:32:38: 6000000 INFO @ Thu, 09 Dec 2021 01:32:40: 11000000 INFO @ Thu, 09 Dec 2021 01:32:44: 7000000 INFO @ Thu, 09 Dec 2021 01:32:44: 1000000 INFO @ Thu, 09 Dec 2021 01:32:46: 12000000 INFO @ Thu, 09 Dec 2021 01:32:49: 8000000 INFO @ Thu, 09 Dec 2021 01:32:50: 2000000 INFO @ Thu, 09 Dec 2021 01:32:52: 13000000 INFO @ Thu, 09 Dec 2021 01:32:54: 9000000 INFO @ Thu, 09 Dec 2021 01:32:55: 3000000 INFO @ Thu, 09 Dec 2021 01:32:58: 14000000 INFO @ Thu, 09 Dec 2021 01:32:59: 10000000 INFO @ Thu, 09 Dec 2021 01:33:01: 4000000 INFO @ Thu, 09 Dec 2021 01:33:04: 15000000 INFO @ Thu, 09 Dec 2021 01:33:04: 11000000 INFO @ Thu, 09 Dec 2021 01:33:07: 5000000 INFO @ Thu, 09 Dec 2021 01:33:09: 12000000 INFO @ Thu, 09 Dec 2021 01:33:10: 16000000 INFO @ Thu, 09 Dec 2021 01:33:13: 6000000 INFO @ Thu, 09 Dec 2021 01:33:15: 13000000 INFO @ Thu, 09 Dec 2021 01:33:15: 17000000 INFO @ Thu, 09 Dec 2021 01:33:19: 7000000 INFO @ Thu, 09 Dec 2021 01:33:20: 14000000 INFO @ Thu, 09 Dec 2021 01:33:21: 18000000 INFO @ Thu, 09 Dec 2021 01:33:24: 8000000 INFO @ Thu, 09 Dec 2021 01:33:25: 15000000 INFO @ Thu, 09 Dec 2021 01:33:27: 19000000 INFO @ Thu, 09 Dec 2021 01:33:30: 16000000 INFO @ Thu, 09 Dec 2021 01:33:30: 9000000 INFO @ Thu, 09 Dec 2021 01:33:33: 20000000 INFO @ Thu, 09 Dec 2021 01:33:35: 17000000 INFO @ Thu, 09 Dec 2021 01:33:36: 10000000 INFO @ Thu, 09 Dec 2021 01:33:39: 21000000 INFO @ Thu, 09 Dec 2021 01:33:40: 18000000 INFO @ Thu, 09 Dec 2021 01:33:42: 11000000 INFO @ Thu, 09 Dec 2021 01:33:45: 22000000 INFO @ Thu, 09 Dec 2021 01:33:45: 19000000 INFO @ Thu, 09 Dec 2021 01:33:47: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:33:47: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:33:47: #1 total tags in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:33:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:33:47: #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 01:33:47: #1 tags after filtering in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:33:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:33:47: #1 finished! INFO @ Thu, 09 Dec 2021 01:33:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:33:48: 12000000 INFO @ Thu, 09 Dec 2021 01:33:48: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 01:33:48: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 01:33:48: start model_add_line... INFO @ Thu, 09 Dec 2021 01:33:48: start X-correlation... INFO @ Thu, 09 Dec 2021 01:33:48: end of X-cor INFO @ Thu, 09 Dec 2021 01:33:48: #2 finished! INFO @ Thu, 09 Dec 2021 01:33:48: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 01:33:48: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 01:33:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05_model.r WARNING @ Thu, 09 Dec 2021 01:33:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:33:48: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 01:33:48: #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 01:33:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:33:51: 20000000 INFO @ Thu, 09 Dec 2021 01:33:54: 13000000 INFO @ Thu, 09 Dec 2021 01:33:56: 21000000 INFO @ Thu, 09 Dec 2021 01:34:00: 14000000 INFO @ Thu, 09 Dec 2021 01:34:01: 22000000 INFO @ Thu, 09 Dec 2021 01:34:02: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:34:02: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:34:02: #1 total tags in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:34:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:34:02: #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 01:34:03: #1 tags after filtering in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:34:03: #1 finished! INFO @ Thu, 09 Dec 2021 01:34:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:34:04: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 01:34:04: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 01:34:04: start model_add_line... INFO @ Thu, 09 Dec 2021 01:34:04: start X-correlation... INFO @ Thu, 09 Dec 2021 01:34:04: end of X-cor INFO @ Thu, 09 Dec 2021 01:34:04: #2 finished! INFO @ Thu, 09 Dec 2021 01:34:04: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 01:34:04: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 01:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10_model.r WARNING @ Thu, 09 Dec 2021 01:34:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:34:04: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 01:34:04: #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 01:34:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:34:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:34:11: 16000000 INFO @ Thu, 09 Dec 2021 01:34:17: 17000000 INFO @ Thu, 09 Dec 2021 01:34:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:34:23: 18000000 INFO @ Thu, 09 Dec 2021 01:34:28: 19000000 INFO @ Thu, 09 Dec 2021 01:34:34: 20000000 INFO @ Thu, 09 Dec 2021 01:34:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:34:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:34:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:34:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.05_summits.bed INFO @ Thu, 09 Dec 2021 01:34:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4955 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:34:40: 21000000 INFO @ Thu, 09 Dec 2021 01:34:45: 22000000 INFO @ Thu, 09 Dec 2021 01:34:47: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:34:47: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:34:47: #1 total tags in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:34:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:34:47: #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 01:34:48: #1 tags after filtering in treatment: 22283047 INFO @ Thu, 09 Dec 2021 01:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:34:48: #1 finished! INFO @ Thu, 09 Dec 2021 01:34:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:34:49: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 01:34:49: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 01:34:49: start model_add_line... INFO @ Thu, 09 Dec 2021 01:34:49: start X-correlation... INFO @ Thu, 09 Dec 2021 01:34:49: end of X-cor INFO @ Thu, 09 Dec 2021 01:34:49: #2 finished! INFO @ Thu, 09 Dec 2021 01:34:49: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 01:34:49: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 01:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20_model.r WARNING @ Thu, 09 Dec 2021 01:34:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:34:49: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 01:34:49: #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 01:34:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:34:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.10_summits.bed INFO @ Thu, 09 Dec 2021 01:34:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:35:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832063/SRX8832063.20_summits.bed INFO @ Thu, 09 Dec 2021 01:35:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling