Job ID = 6507742 SRX = SRX2011720 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:01:10 prefetch.2.10.7: 1) Downloading 'SRR4017962'... 2020-06-26T13:01:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:07:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:07:07 prefetch.2.10.7: 1) 'SRR4017962' was downloaded successfully Read 16373839 spots for SRR4017962/SRR4017962.sra Written 16373839 spots for SRR4017962/SRR4017962.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: 00:26:07 16373839 reads; of these: 16373839 (100.00%) were paired; of these: 2046616 (12.50%) aligned concordantly 0 times 12332690 (75.32%) aligned concordantly exactly 1 time 1994533 (12.18%) aligned concordantly >1 times ---- 2046616 pairs aligned concordantly 0 times; of these: 1491973 (72.90%) aligned discordantly 1 time ---- 554643 pairs aligned 0 times concordantly or discordantly; of these: 1109286 mates make up the pairs; of these: 403574 (36.38%) aligned 0 times 330346 (29.78%) aligned exactly 1 time 375366 (33.84%) aligned >1 times 98.77% overall alignment rate Time searching: 00:26:07 Overall time: 00:26:07 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 16 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] 2411188 / 15679869 = 0.1538 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 @ Fri, 26 Jun 2020 22:51:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.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 @ Fri, 26 Jun 2020 22:51:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:30: 1000000 INFO @ Fri, 26 Jun 2020 22:51:37: 2000000 INFO @ Fri, 26 Jun 2020 22:51:44: 3000000 INFO @ Fri, 26 Jun 2020 22:51:50: 4000000 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 @ Fri, 26 Jun 2020 22:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.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 @ Fri, 26 Jun 2020 22:51:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:57: 5000000 INFO @ Fri, 26 Jun 2020 22:52:02: 1000000 INFO @ Fri, 26 Jun 2020 22:52:05: 6000000 INFO @ Fri, 26 Jun 2020 22:52:11: 2000000 INFO @ Fri, 26 Jun 2020 22:52:12: 7000000 INFO @ Fri, 26 Jun 2020 22:52:19: 8000000 INFO @ Fri, 26 Jun 2020 22:52:19: 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 @ Fri, 26 Jun 2020 22:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.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 @ Fri, 26 Jun 2020 22:52:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:52:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:52:26: 9000000 INFO @ Fri, 26 Jun 2020 22:52:28: 4000000 INFO @ Fri, 26 Jun 2020 22:52:31: 1000000 INFO @ Fri, 26 Jun 2020 22:52:34: 10000000 INFO @ Fri, 26 Jun 2020 22:52:37: 5000000 INFO @ Fri, 26 Jun 2020 22:52:38: 2000000 INFO @ Fri, 26 Jun 2020 22:52:41: 11000000 INFO @ Fri, 26 Jun 2020 22:52:45: 6000000 INFO @ Fri, 26 Jun 2020 22:52:46: 3000000 INFO @ Fri, 26 Jun 2020 22:52:49: 12000000 INFO @ Fri, 26 Jun 2020 22:52:53: 4000000 INFO @ Fri, 26 Jun 2020 22:52:54: 7000000 INFO @ Fri, 26 Jun 2020 22:52:56: 13000000 INFO @ Fri, 26 Jun 2020 22:53:01: 5000000 INFO @ Fri, 26 Jun 2020 22:53:02: 8000000 INFO @ Fri, 26 Jun 2020 22:53:04: 14000000 INFO @ Fri, 26 Jun 2020 22:53:08: 6000000 INFO @ Fri, 26 Jun 2020 22:53:11: 9000000 INFO @ Fri, 26 Jun 2020 22:53:11: 15000000 INFO @ Fri, 26 Jun 2020 22:53:15: 7000000 INFO @ Fri, 26 Jun 2020 22:53:19: 16000000 INFO @ Fri, 26 Jun 2020 22:53:20: 10000000 INFO @ Fri, 26 Jun 2020 22:53:23: 8000000 INFO @ Fri, 26 Jun 2020 22:53:26: 17000000 INFO @ Fri, 26 Jun 2020 22:53:28: 11000000 INFO @ Fri, 26 Jun 2020 22:53:30: 9000000 INFO @ Fri, 26 Jun 2020 22:53:34: 18000000 INFO @ Fri, 26 Jun 2020 22:53:37: 12000000 INFO @ Fri, 26 Jun 2020 22:53:37: 10000000 INFO @ Fri, 26 Jun 2020 22:53:41: 19000000 INFO @ Fri, 26 Jun 2020 22:53:45: 11000000 INFO @ Fri, 26 Jun 2020 22:53:46: 13000000 INFO @ Fri, 26 Jun 2020 22:53:49: 20000000 INFO @ Fri, 26 Jun 2020 22:53:52: 12000000 INFO @ Fri, 26 Jun 2020 22:53:54: 14000000 INFO @ Fri, 26 Jun 2020 22:53:56: 21000000 INFO @ Fri, 26 Jun 2020 22:54:00: 13000000 INFO @ Fri, 26 Jun 2020 22:54:03: 15000000 INFO @ Fri, 26 Jun 2020 22:54:03: 22000000 INFO @ Fri, 26 Jun 2020 22:54:07: 14000000 INFO @ Fri, 26 Jun 2020 22:54:11: 23000000 INFO @ Fri, 26 Jun 2020 22:54:11: 16000000 INFO @ Fri, 26 Jun 2020 22:54:15: 15000000 INFO @ Fri, 26 Jun 2020 22:54:18: 24000000 INFO @ Fri, 26 Jun 2020 22:54:20: 17000000 INFO @ Fri, 26 Jun 2020 22:54:22: 16000000 INFO @ Fri, 26 Jun 2020 22:54:26: 25000000 INFO @ Fri, 26 Jun 2020 22:54:28: 18000000 INFO @ Fri, 26 Jun 2020 22:54:30: 17000000 INFO @ Fri, 26 Jun 2020 22:54:33: 26000000 INFO @ Fri, 26 Jun 2020 22:54:37: 19000000 INFO @ Fri, 26 Jun 2020 22:54:37: 18000000 INFO @ Fri, 26 Jun 2020 22:54:41: 27000000 INFO @ Fri, 26 Jun 2020 22:54:45: 19000000 INFO @ Fri, 26 Jun 2020 22:54:45: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:54:45: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:54:45: #1 total tags in treatment: 11998138 INFO @ Fri, 26 Jun 2020 22:54:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:54:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:54:45: #1 tags after filtering in treatment: 10906286 INFO @ Fri, 26 Jun 2020 22:54:45: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:54:45: #1 finished! INFO @ Fri, 26 Jun 2020 22:54:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:54:45: 20000000 INFO @ Fri, 26 Jun 2020 22:54:46: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 22:54:46: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 22:54:46: start model_add_line... INFO @ Fri, 26 Jun 2020 22:54:46: start X-correlation... INFO @ Fri, 26 Jun 2020 22:54:46: end of X-cor INFO @ Fri, 26 Jun 2020 22:54:46: #2 finished! INFO @ Fri, 26 Jun 2020 22:54:46: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 22:54:46: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 22:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05_model.r WARNING @ Fri, 26 Jun 2020 22:54:46: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:54:46: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 22:54:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:54:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:54:52: 20000000 INFO @ Fri, 26 Jun 2020 22:54:54: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:55:00: 21000000 INFO @ Fri, 26 Jun 2020 22:55:02: 22000000 INFO @ Fri, 26 Jun 2020 22:55:07: 22000000 INFO @ Fri, 26 Jun 2020 22:55:10: 23000000 INFO @ Fri, 26 Jun 2020 22:55:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:55:15: 23000000 INFO @ Fri, 26 Jun 2020 22:55:18: 24000000 INFO @ Fri, 26 Jun 2020 22:55:22: 24000000 INFO @ Fri, 26 Jun 2020 22:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.05_summits.bed INFO @ Fri, 26 Jun 2020 22:55:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:55:26: 25000000 INFO @ Fri, 26 Jun 2020 22:55:30: 25000000 INFO @ Fri, 26 Jun 2020 22:55:35: 26000000 INFO @ Fri, 26 Jun 2020 22:55:37: 26000000 INFO @ Fri, 26 Jun 2020 22:55:43: 27000000 INFO @ Fri, 26 Jun 2020 22:55:45: 27000000 INFO @ Fri, 26 Jun 2020 22:55:47: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:55:47: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:55:47: #1 total tags in treatment: 11998138 INFO @ Fri, 26 Jun 2020 22:55:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:55:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:55:47: #1 tags after filtering in treatment: 10906286 INFO @ Fri, 26 Jun 2020 22:55:47: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:55:47: #1 finished! INFO @ Fri, 26 Jun 2020 22:55:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:55:48: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 22:55:48: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 22:55:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:55:48: start X-correlation... INFO @ Fri, 26 Jun 2020 22:55:48: end of X-cor INFO @ Fri, 26 Jun 2020 22:55:48: #2 finished! INFO @ Fri, 26 Jun 2020 22:55:48: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 22:55:48: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 22:55:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10_model.r WARNING @ Fri, 26 Jun 2020 22:55:48: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:55:48: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 22:55:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:55:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:55:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:55:48: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:55:48: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:55:48: #1 total tags in treatment: 11998138 INFO @ Fri, 26 Jun 2020 22:55:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:55:49: #1 tags after filtering in treatment: 10906286 INFO @ Fri, 26 Jun 2020 22:55:49: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:55:49: #1 finished! INFO @ Fri, 26 Jun 2020 22:55:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:55:49: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 22:55:49: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 22:55:49: start model_add_line... INFO @ Fri, 26 Jun 2020 22:55:50: start X-correlation... INFO @ Fri, 26 Jun 2020 22:55:50: end of X-cor INFO @ Fri, 26 Jun 2020 22:55:50: #2 finished! INFO @ Fri, 26 Jun 2020 22:55:50: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 22:55:50: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 22:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20_model.r WARNING @ Fri, 26 Jun 2020 22:55:50: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:55:50: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 22:55:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:55:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:55:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:56:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:56:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.10_summits.bed INFO @ Fri, 26 Jun 2020 22:56:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011720/SRX2011720.20_summits.bed INFO @ Fri, 26 Jun 2020 22:56:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling