Job ID = 6368720 SRX = SRX5402744 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:05 prefetch.2.10.7: 1) Downloading 'SRR8602978'... 2020-06-16T00:37:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:32 prefetch.2.10.7: 1) 'SRR8602978' was downloaded successfully Read 49034372 spots for SRR8602978/SRR8602978.sra Written 49034372 spots for SRR8602978/SRR8602978.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: 00:10:49 49034372 reads; of these: 49034372 (100.00%) were unpaired; of these: 10667166 (21.75%) aligned 0 times 26646256 (54.34%) aligned exactly 1 time 11720950 (23.90%) aligned >1 times 78.25% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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_rmdupse_core] 10771872 / 38367206 = 0.2808 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 10:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.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 10:03:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:03:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:03:52: 1000000 INFO @ Tue, 16 Jun 2020 10:03:58: 2000000 INFO @ Tue, 16 Jun 2020 10:04:04: 3000000 INFO @ Tue, 16 Jun 2020 10:04:10: 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 10:04:16: 5000000 INFO @ Tue, 16 Jun 2020 10:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.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 10:04:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:23: 6000000 INFO @ Tue, 16 Jun 2020 10:04:23: 1000000 INFO @ Tue, 16 Jun 2020 10:04:29: 7000000 INFO @ Tue, 16 Jun 2020 10:04:29: 2000000 INFO @ Tue, 16 Jun 2020 10:04:35: 8000000 INFO @ Tue, 16 Jun 2020 10:04:36: 3000000 INFO @ Tue, 16 Jun 2020 10:04:42: 9000000 INFO @ Tue, 16 Jun 2020 10:04:42: 4000000 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 10:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.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 10:04:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:48: 10000000 INFO @ Tue, 16 Jun 2020 10:04:49: 5000000 INFO @ Tue, 16 Jun 2020 10:04:53: 1000000 INFO @ Tue, 16 Jun 2020 10:04:55: 11000000 INFO @ Tue, 16 Jun 2020 10:04:55: 6000000 INFO @ Tue, 16 Jun 2020 10:05:00: 2000000 INFO @ Tue, 16 Jun 2020 10:05:01: 12000000 INFO @ Tue, 16 Jun 2020 10:05:02: 7000000 INFO @ Tue, 16 Jun 2020 10:05:06: 3000000 INFO @ Tue, 16 Jun 2020 10:05:08: 13000000 INFO @ Tue, 16 Jun 2020 10:05:08: 8000000 INFO @ Tue, 16 Jun 2020 10:05:13: 4000000 INFO @ Tue, 16 Jun 2020 10:05:15: 14000000 INFO @ Tue, 16 Jun 2020 10:05:15: 9000000 INFO @ Tue, 16 Jun 2020 10:05:20: 5000000 INFO @ Tue, 16 Jun 2020 10:05:21: 15000000 INFO @ Tue, 16 Jun 2020 10:05:22: 10000000 INFO @ Tue, 16 Jun 2020 10:05:26: 6000000 INFO @ Tue, 16 Jun 2020 10:05:28: 16000000 INFO @ Tue, 16 Jun 2020 10:05:28: 11000000 INFO @ Tue, 16 Jun 2020 10:05:33: 7000000 INFO @ Tue, 16 Jun 2020 10:05:34: 17000000 INFO @ Tue, 16 Jun 2020 10:05:35: 12000000 INFO @ Tue, 16 Jun 2020 10:05:39: 8000000 INFO @ Tue, 16 Jun 2020 10:05:41: 18000000 INFO @ Tue, 16 Jun 2020 10:05:42: 13000000 INFO @ Tue, 16 Jun 2020 10:05:46: 9000000 INFO @ Tue, 16 Jun 2020 10:05:48: 19000000 INFO @ Tue, 16 Jun 2020 10:05:49: 14000000 INFO @ Tue, 16 Jun 2020 10:05:52: 10000000 INFO @ Tue, 16 Jun 2020 10:05:55: 20000000 INFO @ Tue, 16 Jun 2020 10:05:56: 15000000 INFO @ Tue, 16 Jun 2020 10:05:59: 11000000 INFO @ Tue, 16 Jun 2020 10:06:01: 21000000 INFO @ Tue, 16 Jun 2020 10:06:03: 16000000 INFO @ Tue, 16 Jun 2020 10:06:06: 12000000 INFO @ Tue, 16 Jun 2020 10:06:08: 22000000 INFO @ Tue, 16 Jun 2020 10:06:09: 17000000 INFO @ Tue, 16 Jun 2020 10:06:12: 13000000 INFO @ Tue, 16 Jun 2020 10:06:15: 23000000 INFO @ Tue, 16 Jun 2020 10:06:16: 18000000 INFO @ Tue, 16 Jun 2020 10:06:19: 14000000 INFO @ Tue, 16 Jun 2020 10:06:21: 24000000 INFO @ Tue, 16 Jun 2020 10:06:23: 19000000 INFO @ Tue, 16 Jun 2020 10:06:25: 15000000 INFO @ Tue, 16 Jun 2020 10:06:28: 25000000 INFO @ Tue, 16 Jun 2020 10:06:30: 20000000 INFO @ Tue, 16 Jun 2020 10:06:32: 16000000 INFO @ Tue, 16 Jun 2020 10:06:34: 26000000 INFO @ Tue, 16 Jun 2020 10:06:37: 21000000 INFO @ Tue, 16 Jun 2020 10:06:39: 17000000 INFO @ Tue, 16 Jun 2020 10:06:41: 27000000 INFO @ Tue, 16 Jun 2020 10:06:44: 22000000 INFO @ Tue, 16 Jun 2020 10:06:45: 18000000 INFO @ Tue, 16 Jun 2020 10:06:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:06:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:06:45: #1 total tags in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:06:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:45: #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 10:06:46: #1 tags after filtering in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:46: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:48: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 10:06:48: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 10:06:48: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:48: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:48: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:48: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:48: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:06:48: #2 alternative fragment length(s) may be 1,21,561 bps INFO @ Tue, 16 Jun 2020 10:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05_model.r WARNING @ Tue, 16 Jun 2020 10:06:48: #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 10:06:48: #2 You may need to consider one of the other alternative d(s): 1,21,561 WARNING @ Tue, 16 Jun 2020 10:06:48: #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 10:06:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:06:51: 23000000 INFO @ Tue, 16 Jun 2020 10:06:52: 19000000 INFO @ Tue, 16 Jun 2020 10:06:57: 24000000 INFO @ Tue, 16 Jun 2020 10:06:58: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:07:04: 25000000 INFO @ Tue, 16 Jun 2020 10:07:04: 21000000 INFO @ Tue, 16 Jun 2020 10:07:11: 26000000 INFO @ Tue, 16 Jun 2020 10:07:11: 22000000 INFO @ Tue, 16 Jun 2020 10:07:17: 27000000 INFO @ Tue, 16 Jun 2020 10:07:17: 23000000 INFO @ Tue, 16 Jun 2020 10:07:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:07:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:07:21: #1 total tags in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:07:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:07:21: #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 10:07:22: #1 tags after filtering in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:07:22: #1 finished! INFO @ Tue, 16 Jun 2020 10:07:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:07:23: 24000000 INFO @ Tue, 16 Jun 2020 10:07:23: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 10:07:23: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 10:07:23: start model_add_line... INFO @ Tue, 16 Jun 2020 10:07:24: start X-correlation... INFO @ Tue, 16 Jun 2020 10:07:24: end of X-cor INFO @ Tue, 16 Jun 2020 10:07:24: #2 finished! INFO @ Tue, 16 Jun 2020 10:07:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:07:24: #2 alternative fragment length(s) may be 1,21,561 bps INFO @ Tue, 16 Jun 2020 10:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10_model.r WARNING @ Tue, 16 Jun 2020 10:07:24: #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 10:07:24: #2 You may need to consider one of the other alternative d(s): 1,21,561 WARNING @ Tue, 16 Jun 2020 10:07:24: #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 10:07:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:07:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:29: 25000000 INFO @ Tue, 16 Jun 2020 10:07:35: 26000000 INFO @ Tue, 16 Jun 2020 10:07:41: 27000000 INFO @ Tue, 16 Jun 2020 10:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.05_summits.bed INFO @ Tue, 16 Jun 2020 10:07:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:07:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:07:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:07:45: #1 total tags in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:07:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:07:45: #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 10:07:45: #1 tags after filtering in treatment: 27595334 INFO @ Tue, 16 Jun 2020 10:07:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:07:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:07:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:07:47: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 10:07:47: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 10:07:47: start model_add_line... INFO @ Tue, 16 Jun 2020 10:07:47: start X-correlation... INFO @ Tue, 16 Jun 2020 10:07:47: end of X-cor INFO @ Tue, 16 Jun 2020 10:07:47: #2 finished! INFO @ Tue, 16 Jun 2020 10:07:47: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:07:47: #2 alternative fragment length(s) may be 1,21,561 bps INFO @ Tue, 16 Jun 2020 10:07:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20_model.r WARNING @ Tue, 16 Jun 2020 10:07:47: #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 10:07:47: #2 You may need to consider one of the other alternative d(s): 1,21,561 WARNING @ Tue, 16 Jun 2020 10:07:47: #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 10:07:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:07:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:08:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:08:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:08:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.10_summits.bed INFO @ Tue, 16 Jun 2020 10:08:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:08:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402744/SRX5402744.20_summits.bed INFO @ Tue, 16 Jun 2020 10:08:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling