Job ID = 6368655 SRX = SRX529215 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:34 prefetch.2.10.7: 1) Downloading 'SRR1265819'... 2020-06-16T00:22:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:10 prefetch.2.10.7: 'SRR1265819' is valid 2020-06-16T00:24:10 prefetch.2.10.7: 1) 'SRR1265819' was downloaded successfully Read 19310035 spots for SRR1265819/SRR1265819.sra Written 19310035 spots for SRR1265819/SRR1265819.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: 00:02:53 19310035 reads; of these: 19310035 (100.00%) were unpaired; of these: 1045040 (5.41%) aligned 0 times 14914588 (77.24%) aligned exactly 1 time 3350407 (17.35%) aligned >1 times 94.59% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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 8 files... [bam_rmdupse_core] 1736185 / 18264995 = 0.0951 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 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.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 09:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:35: 1000000 INFO @ Tue, 16 Jun 2020 09:31:41: 2000000 INFO @ Tue, 16 Jun 2020 09:31:47: 3000000 INFO @ Tue, 16 Jun 2020 09:31:53: 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 09:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.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 09:31:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:00: 5000000 INFO @ Tue, 16 Jun 2020 09:32:05: 1000000 INFO @ Tue, 16 Jun 2020 09:32:06: 6000000 INFO @ Tue, 16 Jun 2020 09:32:11: 2000000 INFO @ Tue, 16 Jun 2020 09:32:13: 7000000 INFO @ Tue, 16 Jun 2020 09:32:17: 3000000 INFO @ Tue, 16 Jun 2020 09:32:20: 8000000 INFO @ Tue, 16 Jun 2020 09:32:23: 4000000 INFO @ Tue, 16 Jun 2020 09:32:27: 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 09:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.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 09:32:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:29: 5000000 INFO @ Tue, 16 Jun 2020 09:32:34: 10000000 INFO @ Tue, 16 Jun 2020 09:32:35: 6000000 INFO @ Tue, 16 Jun 2020 09:32:36: 1000000 INFO @ Tue, 16 Jun 2020 09:32:41: 11000000 INFO @ Tue, 16 Jun 2020 09:32:42: 7000000 INFO @ Tue, 16 Jun 2020 09:32:43: 2000000 INFO @ Tue, 16 Jun 2020 09:32:47: 12000000 INFO @ Tue, 16 Jun 2020 09:32:48: 8000000 INFO @ Tue, 16 Jun 2020 09:32:50: 3000000 INFO @ Tue, 16 Jun 2020 09:32:54: 9000000 INFO @ Tue, 16 Jun 2020 09:32:54: 13000000 INFO @ Tue, 16 Jun 2020 09:32:56: 4000000 INFO @ Tue, 16 Jun 2020 09:33:00: 10000000 INFO @ Tue, 16 Jun 2020 09:33:01: 14000000 INFO @ Tue, 16 Jun 2020 09:33:03: 5000000 INFO @ Tue, 16 Jun 2020 09:33:06: 11000000 INFO @ Tue, 16 Jun 2020 09:33:08: 15000000 INFO @ Tue, 16 Jun 2020 09:33:10: 6000000 INFO @ Tue, 16 Jun 2020 09:33:13: 12000000 INFO @ Tue, 16 Jun 2020 09:33:14: 16000000 INFO @ Tue, 16 Jun 2020 09:33:17: 7000000 INFO @ Tue, 16 Jun 2020 09:33:18: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:33:18: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:33:18: #1 total tags in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:33:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:18: #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 09:33:18: #1 tags after filtering in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:19: 13000000 INFO @ Tue, 16 Jun 2020 09:33:19: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:33:19: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:33:19: #2 alternative fragment length(s) may be 1,26,535 bps INFO @ Tue, 16 Jun 2020 09:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:19: #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 09:33:19: #2 You may need to consider one of the other alternative d(s): 1,26,535 WARNING @ Tue, 16 Jun 2020 09:33:19: #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 09:33:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:24: 8000000 INFO @ Tue, 16 Jun 2020 09:33:25: 14000000 INFO @ Tue, 16 Jun 2020 09:33:31: 9000000 INFO @ Tue, 16 Jun 2020 09:33:31: 15000000 INFO @ Tue, 16 Jun 2020 09:33:37: 10000000 INFO @ Tue, 16 Jun 2020 09:33:38: 16000000 INFO @ Tue, 16 Jun 2020 09:33:41: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:33:41: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:33:41: #1 total tags in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:33:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:41: #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 09:33:41: #1 tags after filtering in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:42: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:33:42: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:33:42: #2 alternative fragment length(s) may be 1,26,535 bps INFO @ Tue, 16 Jun 2020 09:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:42: #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 09:33:42: #2 You may need to consider one of the other alternative d(s): 1,26,535 WARNING @ Tue, 16 Jun 2020 09:33:42: #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 09:33:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:44: 11000000 INFO @ Tue, 16 Jun 2020 09:33:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:50: 12000000 INFO @ Tue, 16 Jun 2020 09:33:57: 13000000 INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:03: 14000000 INFO @ Tue, 16 Jun 2020 09:34:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:09: 15000000 INFO @ Tue, 16 Jun 2020 09:34:15: 16000000 INFO @ Tue, 16 Jun 2020 09:34:18: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:34:18: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:34:18: #1 total tags in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:34:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:18: #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 09:34:18: #1 tags after filtering in treatment: 16528810 INFO @ Tue, 16 Jun 2020 09:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 09:34:19: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2 alternative fragment length(s) may be 1,26,535 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20_model.r WARNING @ Tue, 16 Jun 2020 09:34:19: #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 09:34:19: #2 You may need to consider one of the other alternative d(s): 1,26,535 WARNING @ Tue, 16 Jun 2020 09:34:19: #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 09:34:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529215/SRX529215.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling