Job ID = 8069366 SRX = SRX7217780 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:38 prefetch.2.10.7: 1) Downloading 'SRR10533857'... 2020-08-08T03:31:38 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:31 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:31 prefetch.2.10.7: 1) 'SRR10533857' was downloaded successfully 2020-08-08T03:33:31 prefetch.2.10.7: 'SRR10533857' has 0 unresolved dependencies Read 7231417 spots for SRR10533857/SRR10533857.sra Written 7231417 spots for SRR10533857/SRR10533857.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070251 ("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: 00:12:54 7231417 reads; of these: 7231417 (100.00%) were paired; of these: 1925327 (26.62%) aligned concordantly 0 times 4562401 (63.09%) aligned concordantly exactly 1 time 743689 (10.28%) aligned concordantly >1 times ---- 1925327 pairs aligned concordantly 0 times; of these: 605767 (31.46%) aligned discordantly 1 time ---- 1319560 pairs aligned 0 times concordantly or discordantly; of these: 2639120 mates make up the pairs; of these: 2403078 (91.06%) aligned 0 times 121462 (4.60%) aligned exactly 1 time 114580 (4.34%) aligned >1 times 83.38% overall alignment rate Time searching: 00:12:54 Overall time: 00:12:54 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] 924439 / 5872735 = 0.1574 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 12:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.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 12:52:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:26: 1000000 INFO @ Sat, 08 Aug 2020 12:52:33: 2000000 INFO @ Sat, 08 Aug 2020 12:52:41: 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 @ Sat, 08 Aug 2020 12:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.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 12:52:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:49: 4000000 INFO @ Sat, 08 Aug 2020 12:52:57: 1000000 INFO @ Sat, 08 Aug 2020 12:52:58: 5000000 INFO @ Sat, 08 Aug 2020 12:53:06: 2000000 INFO @ Sat, 08 Aug 2020 12:53:08: 6000000 INFO @ Sat, 08 Aug 2020 12:53:15: 3000000 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 12:53:17: 7000000 INFO @ Sat, 08 Aug 2020 12:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.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 12:53:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:25: 4000000 INFO @ Sat, 08 Aug 2020 12:53:26: 8000000 INFO @ Sat, 08 Aug 2020 12:53:27: 1000000 INFO @ Sat, 08 Aug 2020 12:53:34: 5000000 INFO @ Sat, 08 Aug 2020 12:53:35: 9000000 INFO @ Sat, 08 Aug 2020 12:53:37: 2000000 INFO @ Sat, 08 Aug 2020 12:53:43: 6000000 INFO @ Sat, 08 Aug 2020 12:53:45: 10000000 INFO @ Sat, 08 Aug 2020 12:53:46: 3000000 INFO @ Sat, 08 Aug 2020 12:53:47: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:47: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:47: #1 total tags in treatment: 4460359 INFO @ Sat, 08 Aug 2020 12:53:47: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:47: #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 12:53:47: #1 tags after filtering in treatment: 4109008 INFO @ Sat, 08 Aug 2020 12:53:47: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:53:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:47: #2 number of paired peaks: 398 WARNING @ Sat, 08 Aug 2020 12:53:47: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sat, 08 Aug 2020 12:53:47: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:47: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:47: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:47: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:47: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:53:47: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05_model.r WARNING @ Sat, 08 Aug 2020 12:53:47: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:47: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:53:47: #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 12:53:47: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:53: 7000000 INFO @ Sat, 08 Aug 2020 12:53:56: 4000000 INFO @ Sat, 08 Aug 2020 12:53:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.05_summits.bed INFO @ Sat, 08 Aug 2020 12:54:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:54:02: 8000000 INFO @ Sat, 08 Aug 2020 12:54:05: 5000000 INFO @ Sat, 08 Aug 2020 12:54:11: 9000000 INFO @ Sat, 08 Aug 2020 12:54:14: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:54:20: 10000000 INFO @ Sat, 08 Aug 2020 12:54:22: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:22: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:22: #1 total tags in treatment: 4460359 INFO @ Sat, 08 Aug 2020 12:54:22: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:22: #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 12:54:22: #1 tags after filtering in treatment: 4109008 INFO @ Sat, 08 Aug 2020 12:54:22: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:54:22: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:22: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:22: #2 number of paired peaks: 398 WARNING @ Sat, 08 Aug 2020 12:54:22: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sat, 08 Aug 2020 12:54:22: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:22: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:22: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:22: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:22: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:54:22: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10_model.r WARNING @ Sat, 08 Aug 2020 12:54:22: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:22: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:54:22: #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 12:54:22: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:23: 7000000 INFO @ Sat, 08 Aug 2020 12:54:31: 8000000 INFO @ Sat, 08 Aug 2020 12:54:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.10_summits.bed INFO @ Sat, 08 Aug 2020 12:54:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:54:39: 9000000 INFO @ Sat, 08 Aug 2020 12:54:47: 10000000 INFO @ Sat, 08 Aug 2020 12:54:49: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:49: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:49: #1 total tags in treatment: 4460359 INFO @ Sat, 08 Aug 2020 12:54:49: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:49: #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 12:54:49: #1 tags after filtering in treatment: 4109008 INFO @ Sat, 08 Aug 2020 12:54:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:54:49: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:49: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:49: #2 number of paired peaks: 398 WARNING @ Sat, 08 Aug 2020 12:54:49: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Sat, 08 Aug 2020 12:54:49: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:49: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:49: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:49: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:49: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:54:49: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20_model.r WARNING @ Sat, 08 Aug 2020 12:54:49: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:49: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:54:49: #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 12:54:49: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217780/SRX7217780.20_summits.bed INFO @ Sat, 08 Aug 2020 12:55:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling