Job ID = 14158093 SRX = SRX10040022 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: 00:05:01 25949994 reads; of these: 25949994 (100.00%) were unpaired; of these: 3017118 (11.63%) aligned 0 times 18978799 (73.14%) aligned exactly 1 time 3954077 (15.24%) aligned >1 times 88.37% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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 12 files... [bam_rmdupse_core] 2659366 / 22932876 = 0.1160 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 14:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.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 14:29:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:29:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:29:40: 1000000 INFO @ Wed, 08 Dec 2021 14:29:46: 2000000 INFO @ Wed, 08 Dec 2021 14:29:51: 3000000 INFO @ Wed, 08 Dec 2021 14:29:56: 4000000 INFO @ Wed, 08 Dec 2021 14:30:02: 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 @ Wed, 08 Dec 2021 14:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.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 14:30:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:07: 6000000 INFO @ Wed, 08 Dec 2021 14:30:09: 1000000 INFO @ Wed, 08 Dec 2021 14:30:13: 7000000 INFO @ Wed, 08 Dec 2021 14:30:14: 2000000 INFO @ Wed, 08 Dec 2021 14:30:19: 8000000 INFO @ Wed, 08 Dec 2021 14:30:19: 3000000 INFO @ Wed, 08 Dec 2021 14:30:24: 4000000 INFO @ Wed, 08 Dec 2021 14:30:24: 9000000 INFO @ Wed, 08 Dec 2021 14:30:28: 5000000 INFO @ Wed, 08 Dec 2021 14:30:30: 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 @ Wed, 08 Dec 2021 14:30:33: 6000000 INFO @ Wed, 08 Dec 2021 14:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.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 14:30:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:30:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:30:35: 11000000 INFO @ Wed, 08 Dec 2021 14:30:38: 7000000 INFO @ Wed, 08 Dec 2021 14:30:39: 1000000 INFO @ Wed, 08 Dec 2021 14:30:41: 12000000 INFO @ Wed, 08 Dec 2021 14:30:43: 8000000 INFO @ Wed, 08 Dec 2021 14:30:44: 2000000 INFO @ Wed, 08 Dec 2021 14:30:46: 13000000 INFO @ Wed, 08 Dec 2021 14:30:48: 9000000 INFO @ Wed, 08 Dec 2021 14:30:50: 3000000 INFO @ Wed, 08 Dec 2021 14:30:52: 14000000 INFO @ Wed, 08 Dec 2021 14:30:53: 10000000 INFO @ Wed, 08 Dec 2021 14:30:54: 4000000 INFO @ Wed, 08 Dec 2021 14:30:57: 15000000 INFO @ Wed, 08 Dec 2021 14:30:58: 11000000 INFO @ Wed, 08 Dec 2021 14:30:59: 5000000 INFO @ Wed, 08 Dec 2021 14:31:03: 12000000 INFO @ Wed, 08 Dec 2021 14:31:03: 16000000 INFO @ Wed, 08 Dec 2021 14:31:04: 6000000 INFO @ Wed, 08 Dec 2021 14:31:07: 13000000 INFO @ Wed, 08 Dec 2021 14:31:08: 17000000 INFO @ Wed, 08 Dec 2021 14:31:08: 7000000 INFO @ Wed, 08 Dec 2021 14:31:12: 14000000 INFO @ Wed, 08 Dec 2021 14:31:13: 8000000 INFO @ Wed, 08 Dec 2021 14:31:14: 18000000 INFO @ Wed, 08 Dec 2021 14:31:17: 15000000 INFO @ Wed, 08 Dec 2021 14:31:18: 9000000 INFO @ Wed, 08 Dec 2021 14:31:19: 19000000 INFO @ Wed, 08 Dec 2021 14:31:21: 16000000 INFO @ Wed, 08 Dec 2021 14:31:22: 10000000 INFO @ Wed, 08 Dec 2021 14:31:25: 20000000 INFO @ Wed, 08 Dec 2021 14:31:26: 17000000 INFO @ Wed, 08 Dec 2021 14:31:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:26: #1 total tags in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:31:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:26: #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 14:31:27: #1 tags after filtering in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:27: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:27: 11000000 INFO @ Wed, 08 Dec 2021 14:31:28: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 14:31:28: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:28: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:28: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:28: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:28: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:28: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 14:31:28: #2 alternative fragment length(s) may be 1,49,534,544,548,592 bps INFO @ Wed, 08 Dec 2021 14:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05_model.r WARNING @ Wed, 08 Dec 2021 14:31:28: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:28: #2 You may need to consider one of the other alternative d(s): 1,49,534,544,548,592 WARNING @ Wed, 08 Dec 2021 14:31:28: #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 14:31:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:31: 18000000 INFO @ Wed, 08 Dec 2021 14:31:32: 12000000 INFO @ Wed, 08 Dec 2021 14:31:35: 19000000 INFO @ Wed, 08 Dec 2021 14:31:36: 13000000 INFO @ Wed, 08 Dec 2021 14:31:40: 20000000 INFO @ Wed, 08 Dec 2021 14:31:41: 14000000 INFO @ Wed, 08 Dec 2021 14:31:41: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:31:41: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:31:41: #1 total tags in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:31:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:41: #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 14:31:42: #1 tags after filtering in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:42: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:43: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 14:31:43: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:43: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:43: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:43: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:43: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:43: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 14:31:43: #2 alternative fragment length(s) may be 1,49,534,544,548,592 bps INFO @ Wed, 08 Dec 2021 14:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10_model.r WARNING @ Wed, 08 Dec 2021 14:31:43: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:43: #2 You may need to consider one of the other alternative d(s): 1,49,534,544,548,592 WARNING @ Wed, 08 Dec 2021 14:31:43: #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 14:31:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:45: 15000000 INFO @ Wed, 08 Dec 2021 14:31:50: 16000000 INFO @ Wed, 08 Dec 2021 14:31:54: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:31:59: 18000000 INFO @ Wed, 08 Dec 2021 14:32:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:03: 19000000 INFO @ Wed, 08 Dec 2021 14:32:08: 20000000 INFO @ Wed, 08 Dec 2021 14:32:09: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:32:09: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:32:09: #1 total tags in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:32:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:09: #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 14:32:09: #1 tags after filtering in treatment: 20273510 INFO @ Wed, 08 Dec 2021 14:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:09: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:11: #2 number of paired peaks: 166 WARNING @ Wed, 08 Dec 2021 14:32:11: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 08 Dec 2021 14:32:11: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:11: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:11: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:11: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:11: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 14:32:11: #2 alternative fragment length(s) may be 1,49,534,544,548,592 bps INFO @ Wed, 08 Dec 2021 14:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20_model.r WARNING @ Wed, 08 Dec 2021 14:32:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:32:11: #2 You may need to consider one of the other alternative d(s): 1,49,534,544,548,592 WARNING @ Wed, 08 Dec 2021 14:32:11: #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 14:32:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:32:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.05_summits.bed INFO @ Wed, 08 Dec 2021 14:32:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:32:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.10_summits.bed INFO @ Wed, 08 Dec 2021 14:32:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (403 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:32:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040022/SRX10040022.20_summits.bed INFO @ Wed, 08 Dec 2021 14:32:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (161 records, 4 fields): 1 millis CompletedMACS2peakCalling