Job ID = 6498746 SRX = SRX750069 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:48:07 prefetch.2.10.7: 1) Downloading 'SRR1638751'... 2020-06-25T23:48:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:51:01 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:51:01 prefetch.2.10.7: 1) 'SRR1638751' was downloaded successfully Read 14749445 spots for SRR1638751/SRR1638751.sra Written 14749445 spots for SRR1638751/SRR1638751.sra 2020-06-25T23:52:00 prefetch.2.10.7: 1) Downloading 'SRR1638752'... 2020-06-25T23:52:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:07 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:07 prefetch.2.10.7: 1) 'SRR1638752' was downloaded successfully Read 21298579 spots for SRR1638752/SRR1638752.sra Written 21298579 spots for SRR1638752/SRR1638752.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:48 36048024 reads; of these: 36048024 (100.00%) were unpaired; of these: 1803673 (5.00%) aligned 0 times 21148002 (58.67%) aligned exactly 1 time 13096349 (36.33%) aligned >1 times 95.00% overall alignment rate Time searching: 00:15:50 Overall time: 00:15:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12703601 / 34244351 = 0.3710 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 09:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam'] # control file = None # effective genome size = 1.20e+08 # 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 09:20:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:20:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:20:46: 1000000 INFO @ Fri, 26 Jun 2020 09:20:52: 2000000 INFO @ Fri, 26 Jun 2020 09:20:58: 3000000 INFO @ Fri, 26 Jun 2020 09:21:05: 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 09:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam'] # control file = None # effective genome size = 1.20e+08 # 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 09:21:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:21:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:21:11: 5000000 INFO @ Fri, 26 Jun 2020 09:21:18: 1000000 INFO @ Fri, 26 Jun 2020 09:21:19: 6000000 INFO @ Fri, 26 Jun 2020 09:21:27: 2000000 INFO @ Fri, 26 Jun 2020 09:21:27: 7000000 INFO @ Fri, 26 Jun 2020 09:21:35: 8000000 INFO @ Fri, 26 Jun 2020 09:21:36: 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 09:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.bam'] # control file = None # effective genome size = 1.20e+08 # 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 09:21:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:21:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:21:43: 9000000 INFO @ Fri, 26 Jun 2020 09:21:45: 4000000 INFO @ Fri, 26 Jun 2020 09:21:48: 1000000 INFO @ Fri, 26 Jun 2020 09:21:51: 10000000 INFO @ Fri, 26 Jun 2020 09:21:54: 5000000 INFO @ Fri, 26 Jun 2020 09:21:56: 2000000 INFO @ Fri, 26 Jun 2020 09:21:59: 11000000 INFO @ Fri, 26 Jun 2020 09:22:03: 6000000 INFO @ Fri, 26 Jun 2020 09:22:04: 3000000 INFO @ Fri, 26 Jun 2020 09:22:07: 12000000 INFO @ Fri, 26 Jun 2020 09:22:12: 7000000 INFO @ Fri, 26 Jun 2020 09:22:12: 4000000 INFO @ Fri, 26 Jun 2020 09:22:15: 13000000 INFO @ Fri, 26 Jun 2020 09:22:20: 5000000 INFO @ Fri, 26 Jun 2020 09:22:21: 8000000 INFO @ Fri, 26 Jun 2020 09:22:23: 14000000 INFO @ Fri, 26 Jun 2020 09:22:28: 6000000 INFO @ Fri, 26 Jun 2020 09:22:30: 9000000 INFO @ Fri, 26 Jun 2020 09:22:31: 15000000 INFO @ Fri, 26 Jun 2020 09:22:36: 7000000 INFO @ Fri, 26 Jun 2020 09:22:39: 10000000 INFO @ Fri, 26 Jun 2020 09:22:39: 16000000 INFO @ Fri, 26 Jun 2020 09:22:44: 8000000 INFO @ Fri, 26 Jun 2020 09:22:47: 17000000 INFO @ Fri, 26 Jun 2020 09:22:48: 11000000 INFO @ Fri, 26 Jun 2020 09:22:52: 9000000 INFO @ Fri, 26 Jun 2020 09:22:55: 18000000 INFO @ Fri, 26 Jun 2020 09:22:56: 12000000 INFO @ Fri, 26 Jun 2020 09:23:00: 10000000 INFO @ Fri, 26 Jun 2020 09:23:03: 19000000 INFO @ Fri, 26 Jun 2020 09:23:05: 13000000 INFO @ Fri, 26 Jun 2020 09:23:08: 11000000 INFO @ Fri, 26 Jun 2020 09:23:12: 20000000 INFO @ Fri, 26 Jun 2020 09:23:14: 14000000 INFO @ Fri, 26 Jun 2020 09:23:16: 12000000 INFO @ Fri, 26 Jun 2020 09:23:20: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:23:23: 15000000 INFO @ Fri, 26 Jun 2020 09:23:24: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:23:24: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:23:24: #1 total tags in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:23:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:23:24: #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 09:23:24: #1 tags after filtering in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:23:24: #1 finished! INFO @ Fri, 26 Jun 2020 09:23:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:23:24: 13000000 INFO @ Fri, 26 Jun 2020 09:23:26: #2 number of paired peaks: 148 WARNING @ Fri, 26 Jun 2020 09:23:26: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 26 Jun 2020 09:23:26: start model_add_line... INFO @ Fri, 26 Jun 2020 09:23:26: start X-correlation... INFO @ Fri, 26 Jun 2020 09:23:26: end of X-cor INFO @ Fri, 26 Jun 2020 09:23:26: #2 finished! INFO @ Fri, 26 Jun 2020 09:23:26: #2 predicted fragment length is 63 bps INFO @ Fri, 26 Jun 2020 09:23:26: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 26 Jun 2020 09:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05_model.r WARNING @ Fri, 26 Jun 2020 09:23:26: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:23:26: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 26 Jun 2020 09:23:26: #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 09:23:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:23:31: 16000000 INFO @ Fri, 26 Jun 2020 09:23:32: 14000000 INFO @ Fri, 26 Jun 2020 09:23:40: 17000000 INFO @ Fri, 26 Jun 2020 09:23:41: 15000000 INFO @ Fri, 26 Jun 2020 09:23:49: 16000000 INFO @ Fri, 26 Jun 2020 09:23:49: 18000000 INFO @ Fri, 26 Jun 2020 09:23:57: 17000000 INFO @ Fri, 26 Jun 2020 09:23:58: 19000000 INFO @ Fri, 26 Jun 2020 09:24:05: 18000000 INFO @ Fri, 26 Jun 2020 09:24:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:24:07: 20000000 INFO @ Fri, 26 Jun 2020 09:24:14: 19000000 INFO @ Fri, 26 Jun 2020 09:24:17: 21000000 INFO @ Fri, 26 Jun 2020 09:24:22: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:24:22: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:24:22: #1 total tags in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:24:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:24:22: #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 09:24:22: #1 tags after filtering in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:24:22: #1 finished! INFO @ Fri, 26 Jun 2020 09:24:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:24:22: 20000000 INFO @ Fri, 26 Jun 2020 09:24:23: #2 number of paired peaks: 148 WARNING @ Fri, 26 Jun 2020 09:24:23: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 26 Jun 2020 09:24:23: start model_add_line... INFO @ Fri, 26 Jun 2020 09:24:24: start X-correlation... INFO @ Fri, 26 Jun 2020 09:24:24: end of X-cor INFO @ Fri, 26 Jun 2020 09:24:24: #2 finished! INFO @ Fri, 26 Jun 2020 09:24:24: #2 predicted fragment length is 63 bps INFO @ Fri, 26 Jun 2020 09:24:24: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 26 Jun 2020 09:24:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10_model.r WARNING @ Fri, 26 Jun 2020 09:24:24: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:24:24: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 26 Jun 2020 09:24:24: #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 09:24:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:24:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.05_summits.bed INFO @ Fri, 26 Jun 2020 09:24:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2610 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:24:29: 21000000 INFO @ Fri, 26 Jun 2020 09:24:33: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:24:33: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:24:33: #1 total tags in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:24:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:24:33: #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 09:24:33: #1 tags after filtering in treatment: 21540750 INFO @ Fri, 26 Jun 2020 09:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:24:33: #1 finished! INFO @ Fri, 26 Jun 2020 09:24:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:24:35: #2 number of paired peaks: 148 WARNING @ Fri, 26 Jun 2020 09:24:35: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 26 Jun 2020 09:24:35: start model_add_line... INFO @ Fri, 26 Jun 2020 09:24:35: start X-correlation... INFO @ Fri, 26 Jun 2020 09:24:35: end of X-cor INFO @ Fri, 26 Jun 2020 09:24:35: #2 finished! INFO @ Fri, 26 Jun 2020 09:24:35: #2 predicted fragment length is 63 bps INFO @ Fri, 26 Jun 2020 09:24:35: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 26 Jun 2020 09:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20_model.r WARNING @ Fri, 26 Jun 2020 09:24:35: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:24:35: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 26 Jun 2020 09:24:35: #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 09:24:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:25:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.10_summits.bed INFO @ Fri, 26 Jun 2020 09:25:21: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1540 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750069/SRX750069.20_summits.bed INFO @ Fri, 26 Jun 2020 09:25:33: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1011 records, 4 fields): 2 millis CompletedMACS2peakCalling