Job ID = 8069413 SRX = SRX8392414 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:14 prefetch.2.10.7: 1) Downloading 'SRR11842067'... 2020-08-08T03:32:14 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:38:20 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:38:20 prefetch.2.10.7: 1) 'SRR11842067' was downloaded successfully 2020-08-08T03:38:20 prefetch.2.10.7: 'SRR11842067' has 0 unresolved dependencies Read 7316908 spots for SRR11842067/SRR11842067.sra Written 7316908 spots for SRR11842067/SRR11842067.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070501 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:03 7316908 reads; of these: 7316908 (100.00%) were paired; of these: 1478450 (20.21%) aligned concordantly 0 times 4999643 (68.33%) aligned concordantly exactly 1 time 838815 (11.46%) aligned concordantly >1 times ---- 1478450 pairs aligned concordantly 0 times; of these: 419863 (28.40%) aligned discordantly 1 time ---- 1058587 pairs aligned 0 times concordantly or discordantly; of these: 2117174 mates make up the pairs; of these: 1887298 (89.14%) aligned 0 times 128552 (6.07%) aligned exactly 1 time 101324 (4.79%) aligned >1 times 87.10% overall alignment rate Time searching: 00:13:03 Overall time: 00:13:03 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 12 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] 864128 / 6219449 = 0.1389 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 @ Sat, 08 Aug 2020 12:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.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, 08 Aug 2020 12:57:29: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:29: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:40: 1000000 INFO @ Sat, 08 Aug 2020 12:57:49: 2000000 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 @ Sat, 08 Aug 2020 12:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.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, 08 Aug 2020 12:57:59: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:59: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:00: 3000000 INFO @ Sat, 08 Aug 2020 12:58:11: 4000000 INFO @ Sat, 08 Aug 2020 12:58:11: 1000000 INFO @ Sat, 08 Aug 2020 12:58:23: 5000000 INFO @ Sat, 08 Aug 2020 12:58:23: 2000000 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 @ Sat, 08 Aug 2020 12:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.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, 08 Aug 2020 12:58:29: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:29: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:34: 6000000 INFO @ Sat, 08 Aug 2020 12:58:34: 3000000 INFO @ Sat, 08 Aug 2020 12:58:40: 1000000 INFO @ Sat, 08 Aug 2020 12:58:45: 7000000 INFO @ Sat, 08 Aug 2020 12:58:45: 4000000 INFO @ Sat, 08 Aug 2020 12:58:50: 2000000 INFO @ Sat, 08 Aug 2020 12:58:56: 8000000 INFO @ Sat, 08 Aug 2020 12:58:57: 5000000 INFO @ Sat, 08 Aug 2020 12:59:00: 3000000 INFO @ Sat, 08 Aug 2020 12:59:07: 9000000 INFO @ Sat, 08 Aug 2020 12:59:08: 6000000 INFO @ Sat, 08 Aug 2020 12:59:09: 4000000 INFO @ Sat, 08 Aug 2020 12:59:18: 10000000 INFO @ Sat, 08 Aug 2020 12:59:19: 7000000 INFO @ Sat, 08 Aug 2020 12:59:19: 5000000 INFO @ Sat, 08 Aug 2020 12:59:29: 6000000 INFO @ Sat, 08 Aug 2020 12:59:29: 11000000 INFO @ Sat, 08 Aug 2020 12:59:29: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:29: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:29: #1 total tags in treatment: 5017231 INFO @ Sat, 08 Aug 2020 12:59:29: #1 user defined the maximum tags... BedGraph に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:59:30: #1 tags after filtering in treatment: 4694788 INFO @ Sat, 08 Aug 2020 12:59:30: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 12:59:30: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:30: 8000000 INFO @ Sat, 08 Aug 2020 12:59:30: #2 number of paired peaks: 460 WARNING @ Sat, 08 Aug 2020 12:59:30: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sat, 08 Aug 2020 12:59:30: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:30: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:30: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:30: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:30: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 12:59:30: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 12:59:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05_model.r WARNING @ Sat, 08 Aug 2020 12:59:30: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:30: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 12:59:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:59:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:39: 7000000 INFO @ Sat, 08 Aug 2020 12:59:41: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:41: 9000000 INFO @ Sat, 08 Aug 2020 12:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.05_summits.bed INFO @ Sat, 08 Aug 2020 12:59:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:49: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:52: 10000000 INFO @ Sat, 08 Aug 2020 12:59:59: 9000000 INFO @ Sat, 08 Aug 2020 13:00:02: 11000000 INFO @ Sat, 08 Aug 2020 13:00:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:02: #1 total tags in treatment: 5017231 INFO @ Sat, 08 Aug 2020 13:00:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:00:02: #1 tags after filtering in treatment: 4694788 INFO @ Sat, 08 Aug 2020 13:00:02: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 13:00:02: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:03: #2 number of paired peaks: 460 WARNING @ Sat, 08 Aug 2020 13:00:03: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sat, 08 Aug 2020 13:00:03: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:03: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:03: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:03: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:03: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 13:00:03: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 13:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10_model.r WARNING @ Sat, 08 Aug 2020 13:00:03: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:03: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 13:00:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:00:03: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:08: 10000000 INFO @ Sat, 08 Aug 2020 13:00:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:17: 11000000 INFO @ Sat, 08 Aug 2020 13:00:17: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:17: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:17: #1 total tags in treatment: 5017231 INFO @ Sat, 08 Aug 2020 13:00:17: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:00:17: #1 tags after filtering in treatment: 4694788 INFO @ Sat, 08 Aug 2020 13:00:17: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 13:00:17: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:17: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:17: #2 number of paired peaks: 460 WARNING @ Sat, 08 Aug 2020 13:00:17: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sat, 08 Aug 2020 13:00:17: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:17: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:17: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:17: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:17: #2 predicted fragment length is 215 bps INFO @ Sat, 08 Aug 2020 13:00:17: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 08 Aug 2020 13:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20_model.r WARNING @ Sat, 08 Aug 2020 13:00:17: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:17: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 08 Aug 2020 13:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:00:17: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.10_summits.bed INFO @ Sat, 08 Aug 2020 13:00:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (243 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:00:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392414/SRX8392414.20_summits.bed INFO @ Sat, 08 Aug 2020 13:00:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling