Job ID = 16435248 SRX = SRX13336906 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: 00:41:43 24526602 reads; of these: 24526602 (100.00%) were paired; of these: 12540769 (51.13%) aligned concordantly 0 times 10074073 (41.07%) aligned concordantly exactly 1 time 1911760 (7.79%) aligned concordantly >1 times ---- 12540769 pairs aligned concordantly 0 times; of these: 5577780 (44.48%) aligned discordantly 1 time ---- 6962989 pairs aligned 0 times concordantly or discordantly; of these: 13925978 mates make up the pairs; of these: 11773418 (84.54%) aligned 0 times 1015623 (7.29%) aligned exactly 1 time 1136937 (8.16%) aligned >1 times 76.00% overall alignment rate Time searching: 00:41:43 Overall time: 00:41:43 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] 1580036 / 17511102 = 0.0902 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 11:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.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 11:40:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:40:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:40:30: 1000000 INFO @ Tue, 02 Aug 2022 11:40:40: 2000000 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 11:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.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 11:40:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:40:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:40:50: 3000000 INFO @ Tue, 02 Aug 2022 11:41:01: 1000000 INFO @ Tue, 02 Aug 2022 11:41:01: 4000000 INFO @ Tue, 02 Aug 2022 11:41:12: 2000000 INFO @ Tue, 02 Aug 2022 11:41:13: 5000000 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 11:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.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 11:41:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:41:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:41:24: 6000000 INFO @ Tue, 02 Aug 2022 11:41:24: 3000000 INFO @ Tue, 02 Aug 2022 11:41:31: 1000000 INFO @ Tue, 02 Aug 2022 11:41:36: 7000000 INFO @ Tue, 02 Aug 2022 11:41:36: 4000000 INFO @ Tue, 02 Aug 2022 11:41:43: 2000000 INFO @ Tue, 02 Aug 2022 11:41:47: 8000000 INFO @ Tue, 02 Aug 2022 11:41:48: 5000000 INFO @ Tue, 02 Aug 2022 11:41:54: 3000000 INFO @ Tue, 02 Aug 2022 11:41:58: 9000000 INFO @ Tue, 02 Aug 2022 11:41:59: 6000000 INFO @ Tue, 02 Aug 2022 11:42:06: 4000000 INFO @ Tue, 02 Aug 2022 11:42:09: 10000000 INFO @ Tue, 02 Aug 2022 11:42:10: 7000000 INFO @ Tue, 02 Aug 2022 11:42:17: 5000000 INFO @ Tue, 02 Aug 2022 11:42:20: 11000000 INFO @ Tue, 02 Aug 2022 11:42:21: 8000000 INFO @ Tue, 02 Aug 2022 11:42:28: 6000000 INFO @ Tue, 02 Aug 2022 11:42:31: 12000000 INFO @ Tue, 02 Aug 2022 11:42:32: 9000000 INFO @ Tue, 02 Aug 2022 11:42:39: 7000000 INFO @ Tue, 02 Aug 2022 11:42:42: 13000000 INFO @ Tue, 02 Aug 2022 11:42:43: 10000000 INFO @ Tue, 02 Aug 2022 11:42:50: 8000000 INFO @ Tue, 02 Aug 2022 11:42:53: 14000000 INFO @ Tue, 02 Aug 2022 11:42:54: 11000000 INFO @ Tue, 02 Aug 2022 11:43:01: 9000000 INFO @ Tue, 02 Aug 2022 11:43:04: 15000000 INFO @ Tue, 02 Aug 2022 11:43:05: 12000000 INFO @ Tue, 02 Aug 2022 11:43:12: 10000000 INFO @ Tue, 02 Aug 2022 11:43:15: 16000000 INFO @ Tue, 02 Aug 2022 11:43:16: 13000000 INFO @ Tue, 02 Aug 2022 11:43:23: 11000000 INFO @ Tue, 02 Aug 2022 11:43:26: 17000000 INFO @ Tue, 02 Aug 2022 11:43:27: 14000000 INFO @ Tue, 02 Aug 2022 11:43:34: 12000000 INFO @ Tue, 02 Aug 2022 11:43:37: 18000000 INFO @ Tue, 02 Aug 2022 11:43:38: 15000000 INFO @ Tue, 02 Aug 2022 11:43:45: 13000000 INFO @ Tue, 02 Aug 2022 11:43:47: 19000000 INFO @ Tue, 02 Aug 2022 11:43:49: 16000000 INFO @ Tue, 02 Aug 2022 11:43:55: 14000000 INFO @ Tue, 02 Aug 2022 11:43:58: 20000000 INFO @ Tue, 02 Aug 2022 11:43:59: 17000000 INFO @ Tue, 02 Aug 2022 11:44:06: 15000000 INFO @ Tue, 02 Aug 2022 11:44:09: 21000000 INFO @ Tue, 02 Aug 2022 11:44:10: 18000000 INFO @ Tue, 02 Aug 2022 11:44:17: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:44:20: 22000000 INFO @ Tue, 02 Aug 2022 11:44:21: 19000000 INFO @ Tue, 02 Aug 2022 11:44:28: 17000000 INFO @ Tue, 02 Aug 2022 11:44:30: 23000000 INFO @ Tue, 02 Aug 2022 11:44:32: 20000000 INFO @ Tue, 02 Aug 2022 11:44:39: 18000000 INFO @ Tue, 02 Aug 2022 11:44:41: 24000000 INFO @ Tue, 02 Aug 2022 11:44:43: 21000000 INFO @ Tue, 02 Aug 2022 11:44:50: 19000000 INFO @ Tue, 02 Aug 2022 11:44:52: 25000000 INFO @ Tue, 02 Aug 2022 11:44:54: 22000000 INFO @ Tue, 02 Aug 2022 11:45:01: 20000000 INFO @ Tue, 02 Aug 2022 11:45:03: 26000000 INFO @ Tue, 02 Aug 2022 11:45:05: 23000000 INFO @ Tue, 02 Aug 2022 11:45:11: 21000000 INFO @ Tue, 02 Aug 2022 11:45:13: 27000000 INFO @ Tue, 02 Aug 2022 11:45:15: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:45:22: 22000000 INFO @ Tue, 02 Aug 2022 11:45:24: 28000000 INFO @ Tue, 02 Aug 2022 11:45:26: 25000000 INFO @ Tue, 02 Aug 2022 11:45:33: 23000000 INFO @ Tue, 02 Aug 2022 11:45:35: 29000000 INFO @ Tue, 02 Aug 2022 11:45:37: 26000000 INFO @ Tue, 02 Aug 2022 11:45:43: 24000000 INFO @ Tue, 02 Aug 2022 11:45:45: 30000000 INFO @ Tue, 02 Aug 2022 11:45:47: 27000000 INFO @ Tue, 02 Aug 2022 11:45:54: 25000000 INFO @ Tue, 02 Aug 2022 11:45:55: 31000000 INFO @ Tue, 02 Aug 2022 11:45:58: 28000000 INFO @ Tue, 02 Aug 2022 11:46:04: 26000000 INFO @ Tue, 02 Aug 2022 11:46:06: 32000000 INFO @ Tue, 02 Aug 2022 11:46:09: 29000000 INFO @ Tue, 02 Aug 2022 11:46:15: 27000000 INFO @ Tue, 02 Aug 2022 11:46:16: 33000000 INFO @ Tue, 02 Aug 2022 11:46:19: 30000000 INFO @ Tue, 02 Aug 2022 11:46:26: 28000000 INFO @ Tue, 02 Aug 2022 11:46:27: 34000000 INFO @ Tue, 02 Aug 2022 11:46:28: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:46:28: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:46:28: #1 total tags in treatment: 10792178 INFO @ Tue, 02 Aug 2022 11:46:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:46:28: #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 11:46:28: #1 tags after filtering in treatment: 9828157 INFO @ Tue, 02 Aug 2022 11:46:28: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:46:28: #1 finished! INFO @ Tue, 02 Aug 2022 11:46:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:46:29: #2 number of paired peaks: 492 WARNING @ Tue, 02 Aug 2022 11:46:29: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Tue, 02 Aug 2022 11:46:29: start model_add_line... INFO @ Tue, 02 Aug 2022 11:46:29: start X-correlation... INFO @ Tue, 02 Aug 2022 11:46:29: end of X-cor INFO @ Tue, 02 Aug 2022 11:46:29: #2 finished! INFO @ Tue, 02 Aug 2022 11:46:29: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:46:29: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:46:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05_model.r WARNING @ Tue, 02 Aug 2022 11:46:29: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:46:29: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:46:29: #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 11:46:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:46:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:46:30: 31000000 INFO @ Tue, 02 Aug 2022 11:46:37: 29000000 INFO @ Tue, 02 Aug 2022 11:46:41: 32000000 INFO @ Tue, 02 Aug 2022 11:46:47: 30000000 INFO @ Tue, 02 Aug 2022 11:46:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:46:51: 33000000 INFO @ Tue, 02 Aug 2022 11:46:58: 31000000 INFO @ Tue, 02 Aug 2022 11:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.05_summits.bed INFO @ Tue, 02 Aug 2022 11:46:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:47:02: 34000000 INFO @ Tue, 02 Aug 2022 11:47:03: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:47:03: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:47:03: #1 total tags in treatment: 10792178 INFO @ Tue, 02 Aug 2022 11:47:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:47:03: #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 11:47:03: #1 tags after filtering in treatment: 9828157 INFO @ Tue, 02 Aug 2022 11:47:03: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:47:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:47:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:47:04: #2 number of paired peaks: 492 WARNING @ Tue, 02 Aug 2022 11:47:04: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Tue, 02 Aug 2022 11:47:04: start model_add_line... INFO @ Tue, 02 Aug 2022 11:47:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:47:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:47:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:47:04: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:47:04: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:47:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10_model.r WARNING @ Tue, 02 Aug 2022 11:47:04: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:47:04: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:47:04: #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 11:47:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:47:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:47:08: 32000000 INFO @ Tue, 02 Aug 2022 11:47:17: 33000000 INFO @ Tue, 02 Aug 2022 11:47:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:47:26: 34000000 INFO @ Tue, 02 Aug 2022 11:47:26: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:47:26: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:47:26: #1 total tags in treatment: 10792178 INFO @ Tue, 02 Aug 2022 11:47:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:47:26: #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 11:47:27: #1 tags after filtering in treatment: 9828157 INFO @ Tue, 02 Aug 2022 11:47:27: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:47:27: #1 finished! INFO @ Tue, 02 Aug 2022 11:47:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:47:27: #2 number of paired peaks: 492 WARNING @ Tue, 02 Aug 2022 11:47:27: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Tue, 02 Aug 2022 11:47:27: start model_add_line... INFO @ Tue, 02 Aug 2022 11:47:27: start X-correlation... INFO @ Tue, 02 Aug 2022 11:47:27: end of X-cor INFO @ Tue, 02 Aug 2022 11:47:27: #2 finished! INFO @ Tue, 02 Aug 2022 11:47:27: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:47:27: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20_model.r WARNING @ Tue, 02 Aug 2022 11:47:28: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:47:28: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:47:28: #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 11:47:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.10_summits.bed INFO @ Tue, 02 Aug 2022 11:47:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:47:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336906/SRX13336906.20_summits.bed INFO @ Tue, 02 Aug 2022 11:47:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 33 millis CompletedMACS2peakCalling