Job ID = 14159938 SRX = SRX8845642 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: 00:29:19 49704642 reads; of these: 49704642 (100.00%) were paired; of these: 10233699 (20.59%) aligned concordantly 0 times 32556254 (65.50%) aligned concordantly exactly 1 time 6914689 (13.91%) aligned concordantly >1 times ---- 10233699 pairs aligned concordantly 0 times; of these: 894407 (8.74%) aligned discordantly 1 time ---- 9339292 pairs aligned 0 times concordantly or discordantly; of these: 18678584 mates make up the pairs; of these: 17869262 (95.67%) aligned 0 times 403059 (2.16%) aligned exactly 1 time 406263 (2.18%) aligned >1 times 82.02% overall alignment rate Time searching: 00:29:19 Overall time: 00:29:19 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 36 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] 24963454 / 40207280 = 0.6209 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 01:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.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 01:21:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:21:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:21:58: 1000000 INFO @ Thu, 09 Dec 2021 01:22:02: 2000000 INFO @ Thu, 09 Dec 2021 01:22:07: 3000000 INFO @ Thu, 09 Dec 2021 01:22:12: 4000000 INFO @ Thu, 09 Dec 2021 01:22:17: 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 01:22:22: 6000000 INFO @ Thu, 09 Dec 2021 01:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.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 01:22:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:22:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:22:27: 7000000 INFO @ Thu, 09 Dec 2021 01:22:28: 1000000 INFO @ Thu, 09 Dec 2021 01:22:32: 8000000 INFO @ Thu, 09 Dec 2021 01:22:33: 2000000 INFO @ Thu, 09 Dec 2021 01:22:37: 9000000 INFO @ Thu, 09 Dec 2021 01:22:39: 3000000 INFO @ Thu, 09 Dec 2021 01:22:43: 10000000 INFO @ Thu, 09 Dec 2021 01:22:44: 4000000 INFO @ Thu, 09 Dec 2021 01:22:48: 11000000 INFO @ Thu, 09 Dec 2021 01:22:49: 5000000 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 01:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.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 01:22:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:22:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:22:53: 12000000 INFO @ Thu, 09 Dec 2021 01:22:55: 6000000 INFO @ Thu, 09 Dec 2021 01:22:59: 13000000 INFO @ Thu, 09 Dec 2021 01:23:00: 1000000 INFO @ Thu, 09 Dec 2021 01:23:01: 7000000 INFO @ Thu, 09 Dec 2021 01:23:05: 14000000 INFO @ Thu, 09 Dec 2021 01:23:06: 2000000 INFO @ Thu, 09 Dec 2021 01:23:07: 8000000 INFO @ Thu, 09 Dec 2021 01:23:11: 15000000 INFO @ Thu, 09 Dec 2021 01:23:13: 9000000 INFO @ Thu, 09 Dec 2021 01:23:13: 3000000 INFO @ Thu, 09 Dec 2021 01:23:17: 16000000 INFO @ Thu, 09 Dec 2021 01:23:19: 10000000 INFO @ Thu, 09 Dec 2021 01:23:19: 4000000 INFO @ Thu, 09 Dec 2021 01:23:23: 17000000 INFO @ Thu, 09 Dec 2021 01:23:24: 11000000 INFO @ Thu, 09 Dec 2021 01:23:26: 5000000 INFO @ Thu, 09 Dec 2021 01:23:29: 18000000 INFO @ Thu, 09 Dec 2021 01:23:30: 12000000 INFO @ Thu, 09 Dec 2021 01:23:33: 6000000 INFO @ Thu, 09 Dec 2021 01:23:35: 19000000 INFO @ Thu, 09 Dec 2021 01:23:36: 13000000 INFO @ Thu, 09 Dec 2021 01:23:39: 7000000 INFO @ Thu, 09 Dec 2021 01:23:41: 20000000 INFO @ Thu, 09 Dec 2021 01:23:42: 14000000 INFO @ Thu, 09 Dec 2021 01:23:46: 8000000 INFO @ Thu, 09 Dec 2021 01:23:47: 21000000 INFO @ Thu, 09 Dec 2021 01:23:48: 15000000 INFO @ Thu, 09 Dec 2021 01:23:52: 22000000 INFO @ Thu, 09 Dec 2021 01:23:53: 9000000 INFO @ Thu, 09 Dec 2021 01:23:54: 16000000 INFO @ Thu, 09 Dec 2021 01:23:58: 23000000 INFO @ Thu, 09 Dec 2021 01:23:59: 10000000 INFO @ Thu, 09 Dec 2021 01:24:00: 17000000 INFO @ Thu, 09 Dec 2021 01:24:04: 24000000 INFO @ Thu, 09 Dec 2021 01:24:06: 18000000 INFO @ Thu, 09 Dec 2021 01:24:06: 11000000 INFO @ Thu, 09 Dec 2021 01:24:10: 25000000 INFO @ Thu, 09 Dec 2021 01:24:12: 19000000 INFO @ Thu, 09 Dec 2021 01:24:12: 12000000 INFO @ Thu, 09 Dec 2021 01:24:16: 26000000 INFO @ Thu, 09 Dec 2021 01:24:17: 20000000 INFO @ Thu, 09 Dec 2021 01:24:19: 13000000 INFO @ Thu, 09 Dec 2021 01:24:22: 27000000 INFO @ Thu, 09 Dec 2021 01:24:23: 21000000 INFO @ Thu, 09 Dec 2021 01:24:26: 14000000 INFO @ Thu, 09 Dec 2021 01:24:27: 28000000 INFO @ Thu, 09 Dec 2021 01:24:29: 22000000 INFO @ Thu, 09 Dec 2021 01:24:32: 15000000 INFO @ Thu, 09 Dec 2021 01:24:33: 29000000 INFO @ Thu, 09 Dec 2021 01:24:35: 23000000 INFO @ Thu, 09 Dec 2021 01:24:39: 16000000 INFO @ Thu, 09 Dec 2021 01:24:39: 30000000 INFO @ Thu, 09 Dec 2021 01:24:41: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:24:45: 31000000 INFO @ Thu, 09 Dec 2021 01:24:45: 17000000 INFO @ Thu, 09 Dec 2021 01:24:46: 25000000 INFO @ Thu, 09 Dec 2021 01:24:48: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:24:48: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:24:48: #1 total tags in treatment: 14778529 INFO @ Thu, 09 Dec 2021 01:24:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:24:48: #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 01:24:49: #1 tags after filtering in treatment: 10544976 INFO @ Thu, 09 Dec 2021 01:24:49: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 01:24:49: #1 finished! INFO @ Thu, 09 Dec 2021 01:24:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:24:49: #2 number of paired peaks: 448 WARNING @ Thu, 09 Dec 2021 01:24:49: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Thu, 09 Dec 2021 01:24:49: start model_add_line... INFO @ Thu, 09 Dec 2021 01:24:49: start X-correlation... INFO @ Thu, 09 Dec 2021 01:24:49: end of X-cor INFO @ Thu, 09 Dec 2021 01:24:49: #2 finished! INFO @ Thu, 09 Dec 2021 01:24:49: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 01:24:49: #2 alternative fragment length(s) may be 76 bps INFO @ Thu, 09 Dec 2021 01:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05_model.r WARNING @ Thu, 09 Dec 2021 01:24:49: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:24:49: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Thu, 09 Dec 2021 01:24:49: #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 01:24:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:24:52: 18000000 INFO @ Thu, 09 Dec 2021 01:24:52: 26000000 INFO @ Thu, 09 Dec 2021 01:24:58: 27000000 INFO @ Thu, 09 Dec 2021 01:24:59: 19000000 INFO @ Thu, 09 Dec 2021 01:25:03: 28000000 INFO @ Thu, 09 Dec 2021 01:25:05: 20000000 INFO @ Thu, 09 Dec 2021 01:25:09: 29000000 INFO @ Thu, 09 Dec 2021 01:25:10: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:25:12: 21000000 INFO @ Thu, 09 Dec 2021 01:25:15: 30000000 INFO @ Thu, 09 Dec 2021 01:25:18: 22000000 INFO @ Thu, 09 Dec 2021 01:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.05_summits.bed INFO @ Thu, 09 Dec 2021 01:25:19: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6759 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:25:20: 31000000 INFO @ Thu, 09 Dec 2021 01:25:24: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:25:24: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:25:24: #1 total tags in treatment: 14778529 INFO @ Thu, 09 Dec 2021 01:25:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:25:24: #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 01:25:24: #1 tags after filtering in treatment: 10544976 INFO @ Thu, 09 Dec 2021 01:25:24: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 01:25:24: #1 finished! INFO @ Thu, 09 Dec 2021 01:25:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:25:25: #2 number of paired peaks: 448 WARNING @ Thu, 09 Dec 2021 01:25:25: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Thu, 09 Dec 2021 01:25:25: start model_add_line... INFO @ Thu, 09 Dec 2021 01:25:25: start X-correlation... INFO @ Thu, 09 Dec 2021 01:25:25: 23000000 INFO @ Thu, 09 Dec 2021 01:25:25: end of X-cor INFO @ Thu, 09 Dec 2021 01:25:25: #2 finished! INFO @ Thu, 09 Dec 2021 01:25:25: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 01:25:25: #2 alternative fragment length(s) may be 76 bps INFO @ Thu, 09 Dec 2021 01:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10_model.r WARNING @ Thu, 09 Dec 2021 01:25:25: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:25:25: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Thu, 09 Dec 2021 01:25:25: #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 01:25:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:25:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:25:31: 24000000 INFO @ Thu, 09 Dec 2021 01:25:37: 25000000 INFO @ Thu, 09 Dec 2021 01:25:43: 26000000 INFO @ Thu, 09 Dec 2021 01:25:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:25:49: 27000000 INFO @ Thu, 09 Dec 2021 01:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.10_summits.bed INFO @ Thu, 09 Dec 2021 01:25:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4050 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:25:55: 28000000 INFO @ Thu, 09 Dec 2021 01:26:01: 29000000 INFO @ Thu, 09 Dec 2021 01:26:08: 30000000 INFO @ Thu, 09 Dec 2021 01:26:14: 31000000 INFO @ Thu, 09 Dec 2021 01:26:17: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 01:26:17: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 01:26:17: #1 total tags in treatment: 14778529 INFO @ Thu, 09 Dec 2021 01:26:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:26:17: #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 01:26:17: #1 tags after filtering in treatment: 10544976 INFO @ Thu, 09 Dec 2021 01:26:17: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 09 Dec 2021 01:26:17: #1 finished! INFO @ Thu, 09 Dec 2021 01:26:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:26:18: #2 number of paired peaks: 448 WARNING @ Thu, 09 Dec 2021 01:26:18: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Thu, 09 Dec 2021 01:26:18: start model_add_line... INFO @ Thu, 09 Dec 2021 01:26:18: start X-correlation... INFO @ Thu, 09 Dec 2021 01:26:18: end of X-cor INFO @ Thu, 09 Dec 2021 01:26:18: #2 finished! INFO @ Thu, 09 Dec 2021 01:26:18: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 01:26:18: #2 alternative fragment length(s) may be 76 bps INFO @ Thu, 09 Dec 2021 01:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20_model.r WARNING @ Thu, 09 Dec 2021 01:26:18: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:26:18: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Thu, 09 Dec 2021 01:26:18: #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 01:26:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:26:38: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845642/SRX8845642.20_summits.bed INFO @ Thu, 09 Dec 2021 01:26:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1592 records, 4 fields): 3 millis CompletedMACS2peakCalling