Job ID = 6368197 SRX = SRX494881 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:03:15 prefetch.2.10.7: 1) Downloading 'SRR1198413'... 2020-06-16T00:03:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:26 prefetch.2.10.7: 1) 'SRR1198413' was downloaded successfully Read 25924428 spots for SRR1198413/SRR1198413.sra Written 25924428 spots for SRR1198413/SRR1198413.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: 00:06:37 25924428 reads; of these: 25924428 (100.00%) were unpaired; of these: 926704 (3.57%) aligned 0 times 20625716 (79.56%) aligned exactly 1 time 4372008 (16.86%) aligned >1 times 96.43% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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_rmdupse_core] 8858843 / 24997724 = 0.3544 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 09:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.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 09:20:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:41: 1000000 INFO @ Tue, 16 Jun 2020 09:20:48: 2000000 INFO @ Tue, 16 Jun 2020 09:20:54: 3000000 INFO @ Tue, 16 Jun 2020 09:21:00: 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 @ Tue, 16 Jun 2020 09:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.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 09:21:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:06: 5000000 INFO @ Tue, 16 Jun 2020 09:21:12: 1000000 INFO @ Tue, 16 Jun 2020 09:21:12: 6000000 INFO @ Tue, 16 Jun 2020 09:21:19: 7000000 INFO @ Tue, 16 Jun 2020 09:21:19: 2000000 INFO @ Tue, 16 Jun 2020 09:21:26: 3000000 INFO @ Tue, 16 Jun 2020 09:21:26: 8000000 INFO @ Tue, 16 Jun 2020 09:21:32: 4000000 INFO @ Tue, 16 Jun 2020 09:21:32: 9000000 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 09:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.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 09:21:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:39: 5000000 INFO @ Tue, 16 Jun 2020 09:21:39: 10000000 INFO @ Tue, 16 Jun 2020 09:21:42: 1000000 INFO @ Tue, 16 Jun 2020 09:21:45: 6000000 INFO @ Tue, 16 Jun 2020 09:21:46: 11000000 INFO @ Tue, 16 Jun 2020 09:21:49: 2000000 INFO @ Tue, 16 Jun 2020 09:21:52: 7000000 INFO @ Tue, 16 Jun 2020 09:21:53: 12000000 INFO @ Tue, 16 Jun 2020 09:21:55: 3000000 INFO @ Tue, 16 Jun 2020 09:21:59: 8000000 INFO @ Tue, 16 Jun 2020 09:22:00: 13000000 INFO @ Tue, 16 Jun 2020 09:22:02: 4000000 INFO @ Tue, 16 Jun 2020 09:22:05: 9000000 INFO @ Tue, 16 Jun 2020 09:22:06: 14000000 INFO @ Tue, 16 Jun 2020 09:22:08: 5000000 INFO @ Tue, 16 Jun 2020 09:22:12: 10000000 INFO @ Tue, 16 Jun 2020 09:22:13: 15000000 INFO @ Tue, 16 Jun 2020 09:22:14: 6000000 INFO @ Tue, 16 Jun 2020 09:22:19: 11000000 INFO @ Tue, 16 Jun 2020 09:22:19: 16000000 INFO @ Tue, 16 Jun 2020 09:22:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:20: #1 total tags in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:22:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:20: #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 09:22:21: #1 tags after filtering in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:21: 7000000 INFO @ Tue, 16 Jun 2020 09:22:22: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 09:22:22: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:22:22: #2 alternative fragment length(s) may be 1,43 bps INFO @ Tue, 16 Jun 2020 09:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05_model.r WARNING @ Tue, 16 Jun 2020 09:22:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:22: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Tue, 16 Jun 2020 09:22:22: #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 09:22:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:25: 12000000 INFO @ Tue, 16 Jun 2020 09:22:27: 8000000 INFO @ Tue, 16 Jun 2020 09:22:32: 13000000 INFO @ Tue, 16 Jun 2020 09:22:34: 9000000 INFO @ Tue, 16 Jun 2020 09:22:38: 14000000 INFO @ Tue, 16 Jun 2020 09:22:40: 10000000 INFO @ Tue, 16 Jun 2020 09:22:45: 15000000 INFO @ Tue, 16 Jun 2020 09:22:46: 11000000 INFO @ Tue, 16 Jun 2020 09:22:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:51: 16000000 INFO @ Tue, 16 Jun 2020 09:22:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:52: #1 total tags in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:22:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:52: #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 09:22:52: 12000000 INFO @ Tue, 16 Jun 2020 09:22:52: #1 tags after filtering in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:54: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 09:22:54: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:22:54: #2 alternative fragment length(s) may be 1,43 bps INFO @ Tue, 16 Jun 2020 09:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10_model.r WARNING @ Tue, 16 Jun 2020 09:22:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:54: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Tue, 16 Jun 2020 09:22:54: #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 09:22:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:58: 13000000 INFO @ Tue, 16 Jun 2020 09:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.05_summits.bed INFO @ Tue, 16 Jun 2020 09:23:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:04: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:10: 15000000 INFO @ Tue, 16 Jun 2020 09:23:16: 16000000 INFO @ Tue, 16 Jun 2020 09:23:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:23:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:23:17: #1 total tags in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:23:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:17: #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 09:23:17: #1 tags after filtering in treatment: 16138881 INFO @ Tue, 16 Jun 2020 09:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:18: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 09:23:18: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:23:19: #2 alternative fragment length(s) may be 1,43 bps INFO @ Tue, 16 Jun 2020 09:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:19: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Tue, 16 Jun 2020 09:23:19: #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 09:23:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494881/SRX494881.20_summits.bed INFO @ Tue, 16 Jun 2020 09:23:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling