Job ID = 6365822 SRX = ERX1485063 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:16:57 prefetch.2.10.7: 1) Downloading 'ERR1414280'... 2020-06-15T22:16:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:27:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:27:56 prefetch.2.10.7: 1) 'ERR1414280' was downloaded successfully Read 32278594 spots for ERR1414280/ERR1414280.sra Written 32278594 spots for ERR1414280/ERR1414280.sra 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: 00:46:07 32278594 reads; of these: 32278594 (100.00%) were paired; of these: 496094 (1.54%) aligned concordantly 0 times 27983665 (86.69%) aligned concordantly exactly 1 time 3798835 (11.77%) aligned concordantly >1 times ---- 496094 pairs aligned concordantly 0 times; of these: 60153 (12.13%) aligned discordantly 1 time ---- 435941 pairs aligned 0 times concordantly or discordantly; of these: 871882 mates make up the pairs; of these: 502036 (57.58%) aligned 0 times 282363 (32.39%) aligned exactly 1 time 87483 (10.03%) aligned >1 times 99.22% overall alignment rate Time searching: 00:46:07 Overall time: 00:46:07 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] 15670314 / 31821718 = 0.4924 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.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, 16 Jun 2020 08:39:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:56: 1000000 INFO @ Tue, 16 Jun 2020 08:40:04: 2000000 INFO @ Tue, 16 Jun 2020 08:40:12: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.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, 16 Jun 2020 08:40:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:20: 4000000 INFO @ Tue, 16 Jun 2020 08:40:26: 1000000 INFO @ Tue, 16 Jun 2020 08:40:28: 5000000 INFO @ Tue, 16 Jun 2020 08:40:33: 2000000 INFO @ Tue, 16 Jun 2020 08:40:37: 6000000 INFO @ Tue, 16 Jun 2020 08:40:41: 3000000 INFO @ Tue, 16 Jun 2020 08:40:45: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:40:48: 4000000 INFO @ Tue, 16 Jun 2020 08:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.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, 16 Jun 2020 08:40:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:53: 8000000 INFO @ Tue, 16 Jun 2020 08:40:55: 5000000 INFO @ Tue, 16 Jun 2020 08:40:56: 1000000 INFO @ Tue, 16 Jun 2020 08:41:01: 9000000 INFO @ Tue, 16 Jun 2020 08:41:02: 6000000 INFO @ Tue, 16 Jun 2020 08:41:03: 2000000 INFO @ Tue, 16 Jun 2020 08:41:09: 7000000 INFO @ Tue, 16 Jun 2020 08:41:09: 10000000 INFO @ Tue, 16 Jun 2020 08:41:11: 3000000 INFO @ Tue, 16 Jun 2020 08:41:16: 8000000 INFO @ Tue, 16 Jun 2020 08:41:18: 11000000 INFO @ Tue, 16 Jun 2020 08:41:18: 4000000 INFO @ Tue, 16 Jun 2020 08:41:23: 9000000 INFO @ Tue, 16 Jun 2020 08:41:25: 5000000 INFO @ Tue, 16 Jun 2020 08:41:26: 12000000 INFO @ Tue, 16 Jun 2020 08:41:30: 10000000 INFO @ Tue, 16 Jun 2020 08:41:32: 6000000 INFO @ Tue, 16 Jun 2020 08:41:34: 13000000 INFO @ Tue, 16 Jun 2020 08:41:38: 11000000 INFO @ Tue, 16 Jun 2020 08:41:39: 7000000 INFO @ Tue, 16 Jun 2020 08:41:42: 14000000 INFO @ Tue, 16 Jun 2020 08:41:45: 12000000 INFO @ Tue, 16 Jun 2020 08:41:46: 8000000 INFO @ Tue, 16 Jun 2020 08:41:50: 15000000 INFO @ Tue, 16 Jun 2020 08:41:52: 13000000 INFO @ Tue, 16 Jun 2020 08:41:53: 9000000 INFO @ Tue, 16 Jun 2020 08:41:58: 16000000 INFO @ Tue, 16 Jun 2020 08:41:59: 14000000 INFO @ Tue, 16 Jun 2020 08:42:00: 10000000 INFO @ Tue, 16 Jun 2020 08:42:05: 17000000 INFO @ Tue, 16 Jun 2020 08:42:06: 15000000 INFO @ Tue, 16 Jun 2020 08:42:07: 11000000 INFO @ Tue, 16 Jun 2020 08:42:12: 18000000 INFO @ Tue, 16 Jun 2020 08:42:13: 16000000 INFO @ Tue, 16 Jun 2020 08:42:14: 12000000 INFO @ Tue, 16 Jun 2020 08:42:20: 19000000 INFO @ Tue, 16 Jun 2020 08:42:21: 17000000 INFO @ Tue, 16 Jun 2020 08:42:21: 13000000 INFO @ Tue, 16 Jun 2020 08:42:27: 20000000 INFO @ Tue, 16 Jun 2020 08:42:28: 14000000 INFO @ Tue, 16 Jun 2020 08:42:29: 18000000 INFO @ Tue, 16 Jun 2020 08:42:34: 21000000 INFO @ Tue, 16 Jun 2020 08:42:35: 15000000 INFO @ Tue, 16 Jun 2020 08:42:38: 19000000 INFO @ Tue, 16 Jun 2020 08:42:41: 22000000 INFO @ Tue, 16 Jun 2020 08:42:42: 16000000 INFO @ Tue, 16 Jun 2020 08:42:46: 20000000 INFO @ Tue, 16 Jun 2020 08:42:48: 23000000 INFO @ Tue, 16 Jun 2020 08:42:50: 17000000 INFO @ Tue, 16 Jun 2020 08:42:55: 21000000 INFO @ Tue, 16 Jun 2020 08:42:55: 24000000 INFO @ Tue, 16 Jun 2020 08:42:58: 18000000 INFO @ Tue, 16 Jun 2020 08:43:02: 25000000 INFO @ Tue, 16 Jun 2020 08:43:03: 22000000 INFO @ Tue, 16 Jun 2020 08:43:07: 19000000 INFO @ Tue, 16 Jun 2020 08:43:09: 26000000 INFO @ Tue, 16 Jun 2020 08:43:12: 23000000 INFO @ Tue, 16 Jun 2020 08:43:15: 20000000 INFO @ Tue, 16 Jun 2020 08:43:16: 27000000 INFO @ Tue, 16 Jun 2020 08:43:20: 24000000 INFO @ Tue, 16 Jun 2020 08:43:23: 28000000 INFO @ Tue, 16 Jun 2020 08:43:23: 21000000 INFO @ Tue, 16 Jun 2020 08:43:28: 25000000 INFO @ Tue, 16 Jun 2020 08:43:30: 29000000 INFO @ Tue, 16 Jun 2020 08:43:32: 22000000 INFO @ Tue, 16 Jun 2020 08:43:36: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:37: 30000000 INFO @ Tue, 16 Jun 2020 08:43:40: 23000000 INFO @ Tue, 16 Jun 2020 08:43:44: 31000000 INFO @ Tue, 16 Jun 2020 08:43:44: 27000000 INFO @ Tue, 16 Jun 2020 08:43:48: 24000000 INFO @ Tue, 16 Jun 2020 08:43:50: 32000000 INFO @ Tue, 16 Jun 2020 08:43:53: 28000000 INFO @ Tue, 16 Jun 2020 08:43:56: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:43:56: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:43:56: #1 total tags in treatment: 16139909 INFO @ Tue, 16 Jun 2020 08:43:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:43:56: #1 tags after filtering in treatment: 14483156 INFO @ Tue, 16 Jun 2020 08:43:56: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:43:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:56: 25000000 INFO @ Tue, 16 Jun 2020 08:43:57: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:43:57: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:57: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 08:43:57: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 16 Jun 2020 08:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05_model.r WARNING @ Tue, 16 Jun 2020 08:43:57: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:57: #2 You may need to consider one of the other alternative d(s): 4,160 WARNING @ Tue, 16 Jun 2020 08:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:43:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:00: 29000000 INFO @ Tue, 16 Jun 2020 08:44:04: 26000000 INFO @ Tue, 16 Jun 2020 08:44:09: 30000000 INFO @ Tue, 16 Jun 2020 08:44:12: 27000000 INFO @ Tue, 16 Jun 2020 08:44:17: 31000000 INFO @ Tue, 16 Jun 2020 08:44:20: 28000000 INFO @ Tue, 16 Jun 2020 08:44:25: 32000000 INFO @ Tue, 16 Jun 2020 08:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:28: 29000000 INFO @ Tue, 16 Jun 2020 08:44:32: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:44:32: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:44:32: #1 total tags in treatment: 16139909 INFO @ Tue, 16 Jun 2020 08:44:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:44:32: #1 tags after filtering in treatment: 14483156 INFO @ Tue, 16 Jun 2020 08:44:32: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:44:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:33: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:44:33: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:33: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 08:44:33: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 16 Jun 2020 08:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10_model.r WARNING @ Tue, 16 Jun 2020 08:44:33: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:33: #2 You may need to consider one of the other alternative d(s): 4,160 WARNING @ Tue, 16 Jun 2020 08:44:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:44:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:37: 30000000 INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4781 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:45: 31000000 INFO @ Tue, 16 Jun 2020 08:44:53: 32000000 INFO @ Tue, 16 Jun 2020 08:44:59: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:44:59: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:44:59: #1 total tags in treatment: 16139909 INFO @ Tue, 16 Jun 2020 08:44:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:44:59: #1 tags after filtering in treatment: 14483156 INFO @ Tue, 16 Jun 2020 08:44:59: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:44:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:00: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:45:00: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:00: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 08:45:00: #2 alternative fragment length(s) may be 4,160 bps INFO @ Tue, 16 Jun 2020 08:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:00: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:00: #2 You may need to consider one of the other alternative d(s): 4,160 WARNING @ Tue, 16 Jun 2020 08:45:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:45:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2584 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1485063/ERX1485063.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1101 records, 4 fields): 4 millis CompletedMACS2peakCalling