Job ID = 16435127 SRX = SRX13336914 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 00:36:17 25551558 reads; of these: 25551558 (100.00%) were paired; of these: 14789815 (57.88%) aligned concordantly 0 times 9737330 (38.11%) aligned concordantly exactly 1 time 1024413 (4.01%) aligned concordantly >1 times ---- 14789815 pairs aligned concordantly 0 times; of these: 6472528 (43.76%) aligned discordantly 1 time ---- 8317287 pairs aligned 0 times concordantly or discordantly; of these: 16634574 mates make up the pairs; of these: 14292707 (85.92%) aligned 0 times 1307111 (7.86%) aligned exactly 1 time 1034756 (6.22%) aligned >1 times 72.03% overall alignment rate Time searching: 00:36:17 Overall time: 00:36:17 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 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1647645 / 17202277 = 0.0958 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.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 @ Tue, 02 Aug 2022 11:29:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:29:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:29:34: 1000000 INFO @ Tue, 02 Aug 2022 11:29:43: 2000000 INFO @ Tue, 02 Aug 2022 11:29:52: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.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 @ Tue, 02 Aug 2022 11:29:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:29:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:30:01: 4000000 INFO @ Tue, 02 Aug 2022 11:30:03: 1000000 INFO @ Tue, 02 Aug 2022 11:30:11: 5000000 INFO @ Tue, 02 Aug 2022 11:30:13: 2000000 INFO @ Tue, 02 Aug 2022 11:30:20: 6000000 INFO @ Tue, 02 Aug 2022 11:30:22: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.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 @ Tue, 02 Aug 2022 11:30:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:30:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:30:29: 7000000 INFO @ Tue, 02 Aug 2022 11:30:31: 4000000 INFO @ Tue, 02 Aug 2022 11:30:33: 1000000 INFO @ Tue, 02 Aug 2022 11:30:38: 8000000 INFO @ Tue, 02 Aug 2022 11:30:40: 5000000 INFO @ Tue, 02 Aug 2022 11:30:41: 2000000 INFO @ Tue, 02 Aug 2022 11:30:48: 9000000 INFO @ Tue, 02 Aug 2022 11:30:48: 6000000 INFO @ Tue, 02 Aug 2022 11:30:50: 3000000 INFO @ Tue, 02 Aug 2022 11:30:57: 10000000 INFO @ Tue, 02 Aug 2022 11:30:57: 7000000 INFO @ Tue, 02 Aug 2022 11:30:58: 4000000 INFO @ Tue, 02 Aug 2022 11:31:06: 8000000 INFO @ Tue, 02 Aug 2022 11:31:06: 11000000 INFO @ Tue, 02 Aug 2022 11:31:07: 5000000 INFO @ Tue, 02 Aug 2022 11:31:14: 9000000 INFO @ Tue, 02 Aug 2022 11:31:15: 6000000 INFO @ Tue, 02 Aug 2022 11:31:15: 12000000 INFO @ Tue, 02 Aug 2022 11:31:23: 10000000 INFO @ Tue, 02 Aug 2022 11:31:24: 7000000 INFO @ Tue, 02 Aug 2022 11:31:25: 13000000 INFO @ Tue, 02 Aug 2022 11:31:32: 11000000 INFO @ Tue, 02 Aug 2022 11:31:33: 8000000 INFO @ Tue, 02 Aug 2022 11:31:34: 14000000 INFO @ Tue, 02 Aug 2022 11:31:40: 12000000 INFO @ Tue, 02 Aug 2022 11:31:41: 9000000 INFO @ Tue, 02 Aug 2022 11:31:43: 15000000 INFO @ Tue, 02 Aug 2022 11:31:49: 13000000 INFO @ Tue, 02 Aug 2022 11:31:50: 10000000 INFO @ Tue, 02 Aug 2022 11:31:52: 16000000 INFO @ Tue, 02 Aug 2022 11:31:58: 14000000 INFO @ Tue, 02 Aug 2022 11:31:59: 11000000 INFO @ Tue, 02 Aug 2022 11:32:02: 17000000 INFO @ Tue, 02 Aug 2022 11:32:07: 15000000 INFO @ Tue, 02 Aug 2022 11:32:07: 12000000 INFO @ Tue, 02 Aug 2022 11:32:11: 18000000 INFO @ Tue, 02 Aug 2022 11:32:16: 13000000 INFO @ Tue, 02 Aug 2022 11:32:16: 16000000 INFO @ Tue, 02 Aug 2022 11:32:21: 19000000 INFO @ Tue, 02 Aug 2022 11:32:25: 14000000 INFO @ Tue, 02 Aug 2022 11:32:25: 17000000 INFO @ Tue, 02 Aug 2022 11:32:30: 20000000 INFO @ Tue, 02 Aug 2022 11:32:34: 15000000 INFO @ Tue, 02 Aug 2022 11:32:34: 18000000 INFO @ Tue, 02 Aug 2022 11:32:40: 21000000 INFO @ Tue, 02 Aug 2022 11:32:42: 16000000 INFO @ Tue, 02 Aug 2022 11:32:43: 19000000 INFO @ Tue, 02 Aug 2022 11:32:49: 22000000 INFO @ Tue, 02 Aug 2022 11:32:51: 17000000 INFO @ Tue, 02 Aug 2022 11:32:53: 20000000 INFO @ Tue, 02 Aug 2022 11:32:59: 23000000 INFO @ Tue, 02 Aug 2022 11:32:59: 18000000 INFO @ Tue, 02 Aug 2022 11:33:02: 21000000 INFO @ Tue, 02 Aug 2022 11:33:08: 19000000 INFO @ Tue, 02 Aug 2022 11:33:08: 24000000 INFO @ Tue, 02 Aug 2022 11:33:11: 22000000 INFO @ Tue, 02 Aug 2022 11:33:16: 20000000 INFO @ Tue, 02 Aug 2022 11:33:18: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:33:20: 23000000 INFO @ Tue, 02 Aug 2022 11:33:25: 21000000 INFO @ Tue, 02 Aug 2022 11:33:28: 26000000 INFO @ Tue, 02 Aug 2022 11:33:30: 24000000 INFO @ Tue, 02 Aug 2022 11:33:33: 22000000 INFO @ Tue, 02 Aug 2022 11:33:38: 27000000 INFO @ Tue, 02 Aug 2022 11:33:39: 25000000 INFO @ Tue, 02 Aug 2022 11:33:42: 23000000 INFO @ Tue, 02 Aug 2022 11:33:48: 28000000 INFO @ Tue, 02 Aug 2022 11:33:49: 26000000 INFO @ Tue, 02 Aug 2022 11:33:50: 24000000 INFO @ Tue, 02 Aug 2022 11:33:58: 29000000 INFO @ Tue, 02 Aug 2022 11:33:58: 25000000 INFO @ Tue, 02 Aug 2022 11:33:59: 27000000 INFO @ Tue, 02 Aug 2022 11:34:07: 26000000 INFO @ Tue, 02 Aug 2022 11:34:08: 30000000 INFO @ Tue, 02 Aug 2022 11:34:08: 28000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:34:15: 27000000 INFO @ Tue, 02 Aug 2022 11:34:18: 31000000 INFO @ Tue, 02 Aug 2022 11:34:18: 29000000 INFO @ Tue, 02 Aug 2022 11:34:23: 28000000 INFO @ Tue, 02 Aug 2022 11:34:28: 30000000 INFO @ Tue, 02 Aug 2022 11:34:28: 32000000 INFO @ Tue, 02 Aug 2022 11:34:31: 29000000 INFO @ Tue, 02 Aug 2022 11:34:37: 31000000 INFO @ Tue, 02 Aug 2022 11:34:38: 33000000 INFO @ Tue, 02 Aug 2022 11:34:39: 30000000 INFO @ Tue, 02 Aug 2022 11:34:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:34:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:34:43: #1 total tags in treatment: 9599887 INFO @ Tue, 02 Aug 2022 11:34:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:34:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:34:43: #1 tags after filtering in treatment: 9170762 INFO @ Tue, 02 Aug 2022 11:34:43: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 11:34:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:34:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:34:44: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:34:44: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:34:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:34:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:34:44: end of X-cor INFO @ Tue, 02 Aug 2022 11:34:44: #2 finished! INFO @ Tue, 02 Aug 2022 11:34:44: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:34:44: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05_model.r WARNING @ Tue, 02 Aug 2022 11:34:44: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:34:44: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:34:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:34:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:34:47: 32000000 INFO @ Tue, 02 Aug 2022 11:34:47: 31000000 INFO @ Tue, 02 Aug 2022 11:34:55: 32000000 INFO @ Tue, 02 Aug 2022 11:34:57: 33000000 INFO @ Tue, 02 Aug 2022 11:35:02: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:35:02: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:35:02: #1 total tags in treatment: 9599887 INFO @ Tue, 02 Aug 2022 11:35:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:35:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:35:02: #1 tags after filtering in treatment: 9170762 INFO @ Tue, 02 Aug 2022 11:35:02: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 11:35:02: #1 finished! INFO @ Tue, 02 Aug 2022 11:35:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:35:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:35:02: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:35:02: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:35:02: start model_add_line... INFO @ Tue, 02 Aug 2022 11:35:02: start X-correlation... INFO @ Tue, 02 Aug 2022 11:35:02: end of X-cor INFO @ Tue, 02 Aug 2022 11:35:02: #2 finished! INFO @ Tue, 02 Aug 2022 11:35:02: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:35:02: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10_model.r WARNING @ Tue, 02 Aug 2022 11:35:02: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:35:02: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:35:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:35:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:35:03: 33000000 INFO @ Tue, 02 Aug 2022 11:35:07: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:35:07: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:35:07: #1 total tags in treatment: 9599887 INFO @ Tue, 02 Aug 2022 11:35:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:35:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:35:07: #1 tags after filtering in treatment: 9170762 INFO @ Tue, 02 Aug 2022 11:35:07: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 11:35:07: #1 finished! INFO @ Tue, 02 Aug 2022 11:35:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:35:08: #2 number of paired peaks: 232 WARNING @ Tue, 02 Aug 2022 11:35:08: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 02 Aug 2022 11:35:08: start model_add_line... INFO @ Tue, 02 Aug 2022 11:35:08: start X-correlation... INFO @ Tue, 02 Aug 2022 11:35:08: end of X-cor INFO @ Tue, 02 Aug 2022 11:35:08: #2 finished! INFO @ Tue, 02 Aug 2022 11:35:08: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:35:08: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20_model.r WARNING @ Tue, 02 Aug 2022 11:35:08: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:35:08: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:35:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:35:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:35:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:35:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:35:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.05_summits.bed INFO @ Tue, 02 Aug 2022 11:35:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (410 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:35:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:35:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.10_summits.bed INFO @ Tue, 02 Aug 2022 11:35:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:35:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:35:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336914/SRX13336914.20_summits.bed INFO @ Tue, 02 Aug 2022 11:35:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 18 millis CompletedMACS2peakCalling