Job ID = 12265399 SRX = SRX3029122 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: 00:27:15 28757519 reads; of these: 28757519 (100.00%) were paired; of these: 10075030 (35.03%) aligned concordantly 0 times 16014149 (55.69%) aligned concordantly exactly 1 time 2668340 (9.28%) aligned concordantly >1 times ---- 10075030 pairs aligned concordantly 0 times; of these: 3230686 (32.07%) aligned discordantly 1 time ---- 6844344 pairs aligned 0 times concordantly or discordantly; of these: 13688688 mates make up the pairs; of these: 12076215 (88.22%) aligned 0 times 700831 (5.12%) aligned exactly 1 time 911642 (6.66%) aligned >1 times 79.00% overall alignment rate Time searching: 00:27:15 Overall time: 00:27:15 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 20 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] 4551382 / 21670730 = 0.2100 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.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 @ Sat, 03 Apr 2021 07:33:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:17: 1000000 INFO @ Sat, 03 Apr 2021 07:33:23: 2000000 INFO @ Sat, 03 Apr 2021 07:33:28: 3000000 INFO @ Sat, 03 Apr 2021 07:33:33: 4000000 INFO @ Sat, 03 Apr 2021 07:33:38: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.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 @ Sat, 03 Apr 2021 07:33:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:43: 6000000 INFO @ Sat, 03 Apr 2021 07:33:48: 1000000 INFO @ Sat, 03 Apr 2021 07:33:49: 7000000 INFO @ Sat, 03 Apr 2021 07:33:53: 2000000 INFO @ Sat, 03 Apr 2021 07:33:54: 8000000 INFO @ Sat, 03 Apr 2021 07:33:58: 3000000 INFO @ Sat, 03 Apr 2021 07:33:59: 9000000 INFO @ Sat, 03 Apr 2021 07:34:04: 4000000 INFO @ Sat, 03 Apr 2021 07:34:05: 10000000 INFO @ Sat, 03 Apr 2021 07:34:09: 5000000 INFO @ Sat, 03 Apr 2021 07:34:10: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.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 @ Sat, 03 Apr 2021 07:34:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:34:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:14: 6000000 INFO @ Sat, 03 Apr 2021 07:34:16: 12000000 INFO @ Sat, 03 Apr 2021 07:34:19: 1000000 INFO @ Sat, 03 Apr 2021 07:34:20: 7000000 INFO @ Sat, 03 Apr 2021 07:34:21: 13000000 INFO @ Sat, 03 Apr 2021 07:34:25: 2000000 INFO @ Sat, 03 Apr 2021 07:34:25: 8000000 INFO @ Sat, 03 Apr 2021 07:34:27: 14000000 INFO @ Sat, 03 Apr 2021 07:34:31: 9000000 INFO @ Sat, 03 Apr 2021 07:34:32: 3000000 INFO @ Sat, 03 Apr 2021 07:34:32: 15000000 INFO @ Sat, 03 Apr 2021 07:34:36: 10000000 INFO @ Sat, 03 Apr 2021 07:34:38: 16000000 INFO @ Sat, 03 Apr 2021 07:34:38: 4000000 INFO @ Sat, 03 Apr 2021 07:34:42: 11000000 INFO @ Sat, 03 Apr 2021 07:34:43: 17000000 INFO @ Sat, 03 Apr 2021 07:34:45: 5000000 INFO @ Sat, 03 Apr 2021 07:34:47: 12000000 INFO @ Sat, 03 Apr 2021 07:34:49: 18000000 INFO @ Sat, 03 Apr 2021 07:34:51: 6000000 INFO @ Sat, 03 Apr 2021 07:34:53: 13000000 INFO @ Sat, 03 Apr 2021 07:34:54: 19000000 INFO @ Sat, 03 Apr 2021 07:34:57: 7000000 INFO @ Sat, 03 Apr 2021 07:34:59: 14000000 INFO @ Sat, 03 Apr 2021 07:35:00: 20000000 INFO @ Sat, 03 Apr 2021 07:35:04: 8000000 INFO @ Sat, 03 Apr 2021 07:35:04: 15000000 INFO @ Sat, 03 Apr 2021 07:35:06: 21000000 INFO @ Sat, 03 Apr 2021 07:35:10: 16000000 INFO @ Sat, 03 Apr 2021 07:35:10: 9000000 INFO @ Sat, 03 Apr 2021 07:35:11: 22000000 INFO @ Sat, 03 Apr 2021 07:35:15: 17000000 INFO @ Sat, 03 Apr 2021 07:35:17: 10000000 INFO @ Sat, 03 Apr 2021 07:35:17: 23000000 INFO @ Sat, 03 Apr 2021 07:35:21: 18000000 INFO @ Sat, 03 Apr 2021 07:35:22: 24000000 INFO @ Sat, 03 Apr 2021 07:35:23: 11000000 INFO @ Sat, 03 Apr 2021 07:35:26: 19000000 INFO @ Sat, 03 Apr 2021 07:35:28: 25000000 INFO @ Sat, 03 Apr 2021 07:35:29: 12000000 INFO @ Sat, 03 Apr 2021 07:35:32: 20000000 INFO @ Sat, 03 Apr 2021 07:35:33: 26000000 INFO @ Sat, 03 Apr 2021 07:35:36: 13000000 INFO @ Sat, 03 Apr 2021 07:35:38: 21000000 INFO @ Sat, 03 Apr 2021 07:35:39: 27000000 INFO @ Sat, 03 Apr 2021 07:35:42: 14000000 INFO @ Sat, 03 Apr 2021 07:35:43: 22000000 INFO @ Sat, 03 Apr 2021 07:35:44: 28000000 INFO @ Sat, 03 Apr 2021 07:35:49: 15000000 INFO @ Sat, 03 Apr 2021 07:35:49: 23000000 INFO @ Sat, 03 Apr 2021 07:35:49: 29000000 INFO @ Sat, 03 Apr 2021 07:35:55: 24000000 INFO @ Sat, 03 Apr 2021 07:35:55: 30000000 INFO @ Sat, 03 Apr 2021 07:35:55: 16000000 INFO @ Sat, 03 Apr 2021 07:36:00: 25000000 INFO @ Sat, 03 Apr 2021 07:36:00: 31000000 INFO @ Sat, 03 Apr 2021 07:36:02: 17000000 INFO @ Sat, 03 Apr 2021 07:36:05: 26000000 INFO @ Sat, 03 Apr 2021 07:36:06: 32000000 INFO @ Sat, 03 Apr 2021 07:36:08: 18000000 INFO @ Sat, 03 Apr 2021 07:36:11: 27000000 INFO @ Sat, 03 Apr 2021 07:36:11: 33000000 INFO @ Sat, 03 Apr 2021 07:36:14: 19000000 INFO @ Sat, 03 Apr 2021 07:36:16: 28000000 INFO @ Sat, 03 Apr 2021 07:36:17: 34000000 INFO @ Sat, 03 Apr 2021 07:36:21: 20000000 INFO @ Sat, 03 Apr 2021 07:36:22: 29000000 INFO @ Sat, 03 Apr 2021 07:36:22: 35000000 INFO @ Sat, 03 Apr 2021 07:36:27: 30000000 INFO @ Sat, 03 Apr 2021 07:36:27: 21000000 INFO @ Sat, 03 Apr 2021 07:36:28: 36000000 INFO @ Sat, 03 Apr 2021 07:36:30: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:36:30: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:36:30: #1 total tags in treatment: 14956023 INFO @ Sat, 03 Apr 2021 07:36:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:36:30: #1 tags after filtering in treatment: 9952565 INFO @ Sat, 03 Apr 2021 07:36:30: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:36:30: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:31: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 07:36:31: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:31: #2 predicted fragment length is 114 bps INFO @ Sat, 03 Apr 2021 07:36:31: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 03 Apr 2021 07:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05_model.r WARNING @ Sat, 03 Apr 2021 07:36:31: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:31: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 03 Apr 2021 07:36:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:36:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:33: 31000000 INFO @ Sat, 03 Apr 2021 07:36:34: 22000000 INFO @ Sat, 03 Apr 2021 07:36:38: 32000000 INFO @ Sat, 03 Apr 2021 07:36:40: 23000000 INFO @ Sat, 03 Apr 2021 07:36:44: 33000000 INFO @ Sat, 03 Apr 2021 07:36:46: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:36:49: 34000000 INFO @ Sat, 03 Apr 2021 07:36:52: 25000000 INFO @ Sat, 03 Apr 2021 07:36:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:55: 35000000 INFO @ Sat, 03 Apr 2021 07:36:59: 26000000 INFO @ Sat, 03 Apr 2021 07:37:00: 36000000 INFO @ Sat, 03 Apr 2021 07:37:02: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:37:02: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:37:02: #1 total tags in treatment: 14956023 INFO @ Sat, 03 Apr 2021 07:37:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:37:02: #1 tags after filtering in treatment: 9952565 INFO @ Sat, 03 Apr 2021 07:37:02: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:37:02: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:03: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 07:37:03: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:03: #2 predicted fragment length is 114 bps INFO @ Sat, 03 Apr 2021 07:37:03: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 03 Apr 2021 07:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10_model.r WARNING @ Sat, 03 Apr 2021 07:37:03: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:03: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 03 Apr 2021 07:37:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:37:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:05: 27000000 INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.05_summits.bed INFO @ Sat, 03 Apr 2021 07:37:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10278 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:11: 28000000 INFO @ Sat, 03 Apr 2021 07:37:17: 29000000 INFO @ Sat, 03 Apr 2021 07:37:23: 30000000 INFO @ Sat, 03 Apr 2021 07:37:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:29: 31000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:37:36: 32000000 INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.10_summits.bed INFO @ Sat, 03 Apr 2021 07:37:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6375 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:42: 33000000 INFO @ Sat, 03 Apr 2021 07:37:48: 34000000 INFO @ Sat, 03 Apr 2021 07:37:54: 35000000 INFO @ Sat, 03 Apr 2021 07:38:00: 36000000 INFO @ Sat, 03 Apr 2021 07:38:02: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:38:02: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:38:02: #1 total tags in treatment: 14956023 INFO @ Sat, 03 Apr 2021 07:38:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:38:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:38:03: #1 tags after filtering in treatment: 9952565 INFO @ Sat, 03 Apr 2021 07:38:03: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:38:03: #1 finished! INFO @ Sat, 03 Apr 2021 07:38:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:38:03: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 07:38:03: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 07:38:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:38:04: start X-correlation... INFO @ Sat, 03 Apr 2021 07:38:04: end of X-cor INFO @ Sat, 03 Apr 2021 07:38:04: #2 finished! INFO @ Sat, 03 Apr 2021 07:38:04: #2 predicted fragment length is 114 bps INFO @ Sat, 03 Apr 2021 07:38:04: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 03 Apr 2021 07:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20_model.r WARNING @ Sat, 03 Apr 2021 07:38:04: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:38:04: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 03 Apr 2021 07:38:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:38:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:38:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:38:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029122/SRX3029122.20_summits.bed INFO @ Sat, 03 Apr 2021 07:38:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3205 records, 4 fields): 5 millis CompletedMACS2peakCalling