Job ID = 6368652 SRX = SRX529212 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:15 prefetch.2.10.7: 1) Downloading 'SRR1265816'... 2020-06-16T00:33:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:17 prefetch.2.10.7: 'SRR1265816' is valid 2020-06-16T00:36:17 prefetch.2.10.7: 1) 'SRR1265816' was downloaded successfully Read 23070060 spots for SRR1265816/SRR1265816.sra Written 23070060 spots for SRR1265816/SRR1265816.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: 00:03:28 23070060 reads; of these: 23070060 (100.00%) were unpaired; of these: 5699476 (24.71%) aligned 0 times 15030430 (65.15%) aligned exactly 1 time 2340154 (10.14%) aligned >1 times 75.29% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 2620798 / 17370584 = 0.1509 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 09:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.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 09:44:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:59: 1000000 INFO @ Tue, 16 Jun 2020 09:45:04: 2000000 INFO @ Tue, 16 Jun 2020 09:45:10: 3000000 INFO @ Tue, 16 Jun 2020 09:45:15: 4000000 INFO @ Tue, 16 Jun 2020 09:45:21: 5000000 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 09:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.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 09:45:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:27: 6000000 INFO @ Tue, 16 Jun 2020 09:45:29: 1000000 INFO @ Tue, 16 Jun 2020 09:45:33: 7000000 INFO @ Tue, 16 Jun 2020 09:45:35: 2000000 INFO @ Tue, 16 Jun 2020 09:45:39: 8000000 INFO @ Tue, 16 Jun 2020 09:45:41: 3000000 INFO @ Tue, 16 Jun 2020 09:45:45: 9000000 INFO @ Tue, 16 Jun 2020 09:45:47: 4000000 INFO @ Tue, 16 Jun 2020 09:45:51: 10000000 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 09:45:53: 5000000 INFO @ Tue, 16 Jun 2020 09:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.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 09:45:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:57: 11000000 INFO @ Tue, 16 Jun 2020 09:45:59: 6000000 INFO @ Tue, 16 Jun 2020 09:45:59: 1000000 INFO @ Tue, 16 Jun 2020 09:46:03: 12000000 INFO @ Tue, 16 Jun 2020 09:46:05: 7000000 INFO @ Tue, 16 Jun 2020 09:46:06: 2000000 INFO @ Tue, 16 Jun 2020 09:46:09: 13000000 INFO @ Tue, 16 Jun 2020 09:46:11: 8000000 INFO @ Tue, 16 Jun 2020 09:46:12: 3000000 INFO @ Tue, 16 Jun 2020 09:46:15: 14000000 INFO @ Tue, 16 Jun 2020 09:46:17: 9000000 INFO @ Tue, 16 Jun 2020 09:46:18: 4000000 INFO @ Tue, 16 Jun 2020 09:46:20: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:46:20: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:46:20: #1 total tags in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:46:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:20: #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 09:46:20: #1 tags after filtering in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:46:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:21: #2 number of paired peaks: 139 WARNING @ Tue, 16 Jun 2020 09:46:21: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:21: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 09:46:21: #2 alternative fragment length(s) may be 2,34,488,495,574 bps INFO @ Tue, 16 Jun 2020 09:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05_model.r WARNING @ Tue, 16 Jun 2020 09:46:21: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:21: #2 You may need to consider one of the other alternative d(s): 2,34,488,495,574 WARNING @ Tue, 16 Jun 2020 09:46:21: #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 09:46:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:23: 10000000 INFO @ Tue, 16 Jun 2020 09:46:24: 5000000 INFO @ Tue, 16 Jun 2020 09:46:29: 11000000 INFO @ Tue, 16 Jun 2020 09:46:30: 6000000 INFO @ Tue, 16 Jun 2020 09:46:35: 12000000 INFO @ Tue, 16 Jun 2020 09:46:36: 7000000 INFO @ Tue, 16 Jun 2020 09:46:41: 13000000 INFO @ Tue, 16 Jun 2020 09:46:42: 8000000 INFO @ Tue, 16 Jun 2020 09:46:47: 14000000 INFO @ Tue, 16 Jun 2020 09:46:48: 9000000 INFO @ Tue, 16 Jun 2020 09:46:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:46:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:46:52: #1 total tags in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:46:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:52: #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 09:46:52: #1 tags after filtering in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:53: #2 number of paired peaks: 139 WARNING @ Tue, 16 Jun 2020 09:46:53: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:53: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 09:46:53: #2 alternative fragment length(s) may be 2,34,488,495,574 bps INFO @ Tue, 16 Jun 2020 09:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:53: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:53: #2 You may need to consider one of the other alternative d(s): 2,34,488,495,574 WARNING @ Tue, 16 Jun 2020 09:46:53: #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 09:46:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:54: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:00: 11000000 INFO @ Tue, 16 Jun 2020 09:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1621 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:06: 12000000 INFO @ Tue, 16 Jun 2020 09:47:12: 13000000 INFO @ Tue, 16 Jun 2020 09:47:17: 14000000 INFO @ Tue, 16 Jun 2020 09:47:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:21: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:47:21: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:47:21: #1 total tags in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:47:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:21: #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 09:47:22: #1 tags after filtering in treatment: 14749786 INFO @ Tue, 16 Jun 2020 09:47:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:23: #2 number of paired peaks: 139 WARNING @ Tue, 16 Jun 2020 09:47:23: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:23: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 09:47:23: #2 alternative fragment length(s) may be 2,34,488,495,574 bps INFO @ Tue, 16 Jun 2020 09:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20_model.r WARNING @ Tue, 16 Jun 2020 09:47:23: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:47:23: #2 You may need to consider one of the other alternative d(s): 2,34,488,495,574 WARNING @ Tue, 16 Jun 2020 09:47:23: #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 09:47:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:47:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529212/SRX529212.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling