Job ID = 6498749 SRX = SRX750072 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:51:36 prefetch.2.10.7: 1) Downloading 'SRR1638756'... 2020-06-25T23:51:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:47 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:47 prefetch.2.10.7: 1) 'SRR1638756' was downloaded successfully Read 35764590 spots for SRR1638756/SRR1638756.sra Written 35764590 spots for SRR1638756/SRR1638756.sra 2020-06-25T23:58:12 prefetch.2.10.7: 1) Downloading 'SRR1638757'... 2020-06-25T23:58:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:00:40 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:00:40 prefetch.2.10.7: 1) 'SRR1638757' was downloaded successfully Read 21272306 spots for SRR1638757/SRR1638757.sra Written 21272306 spots for SRR1638757/SRR1638757.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: 00:26:31 57036896 reads; of these: 57036896 (100.00%) were unpaired; of these: 2526620 (4.43%) aligned 0 times 38031840 (66.68%) aligned exactly 1 time 16478436 (28.89%) aligned >1 times 95.57% overall alignment rate Time searching: 00:26:31 Overall time: 00:26:31 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 24 files... [bam_rmdupse_core] 31007403 / 54510276 = 0.5688 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 09:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.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 09:43:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:16: 1000000 INFO @ Fri, 26 Jun 2020 09:43:22: 2000000 INFO @ Fri, 26 Jun 2020 09:43:28: 3000000 INFO @ Fri, 26 Jun 2020 09:43:34: 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 09:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.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 09:43:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:40: 5000000 INFO @ Fri, 26 Jun 2020 09:43:46: 1000000 INFO @ Fri, 26 Jun 2020 09:43:47: 6000000 INFO @ Fri, 26 Jun 2020 09:43:53: 2000000 INFO @ Fri, 26 Jun 2020 09:43:53: 7000000 INFO @ Fri, 26 Jun 2020 09:43:59: 3000000 INFO @ Fri, 26 Jun 2020 09:43:59: 8000000 INFO @ Fri, 26 Jun 2020 09:44:05: 9000000 INFO @ Fri, 26 Jun 2020 09:44:06: 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 @ Fri, 26 Jun 2020 09:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.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 09:44:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:44:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:44:12: 10000000 INFO @ Fri, 26 Jun 2020 09:44:13: 5000000 INFO @ Fri, 26 Jun 2020 09:44:17: 1000000 INFO @ Fri, 26 Jun 2020 09:44:18: 11000000 INFO @ Fri, 26 Jun 2020 09:44:20: 6000000 INFO @ Fri, 26 Jun 2020 09:44:24: 2000000 INFO @ Fri, 26 Jun 2020 09:44:24: 12000000 INFO @ Fri, 26 Jun 2020 09:44:27: 7000000 INFO @ Fri, 26 Jun 2020 09:44:31: 13000000 INFO @ Fri, 26 Jun 2020 09:44:31: 3000000 INFO @ Fri, 26 Jun 2020 09:44:34: 8000000 INFO @ Fri, 26 Jun 2020 09:44:37: 14000000 INFO @ Fri, 26 Jun 2020 09:44:39: 4000000 INFO @ Fri, 26 Jun 2020 09:44:42: 9000000 INFO @ Fri, 26 Jun 2020 09:44:43: 15000000 INFO @ Fri, 26 Jun 2020 09:44:46: 5000000 INFO @ Fri, 26 Jun 2020 09:44:49: 10000000 INFO @ Fri, 26 Jun 2020 09:44:50: 16000000 INFO @ Fri, 26 Jun 2020 09:44:53: 6000000 INFO @ Fri, 26 Jun 2020 09:44:55: 11000000 INFO @ Fri, 26 Jun 2020 09:44:56: 17000000 INFO @ Fri, 26 Jun 2020 09:45:00: 7000000 INFO @ Fri, 26 Jun 2020 09:45:02: 18000000 INFO @ Fri, 26 Jun 2020 09:45:03: 12000000 INFO @ Fri, 26 Jun 2020 09:45:07: 8000000 INFO @ Fri, 26 Jun 2020 09:45:08: 19000000 INFO @ Fri, 26 Jun 2020 09:45:10: 13000000 INFO @ Fri, 26 Jun 2020 09:45:14: 9000000 INFO @ Fri, 26 Jun 2020 09:45:16: 20000000 INFO @ Fri, 26 Jun 2020 09:45:17: 14000000 INFO @ Fri, 26 Jun 2020 09:45:21: 10000000 INFO @ Fri, 26 Jun 2020 09:45:23: 21000000 INFO @ Fri, 26 Jun 2020 09:45:24: 15000000 INFO @ Fri, 26 Jun 2020 09:45:28: 11000000 INFO @ Fri, 26 Jun 2020 09:45:29: 22000000 INFO @ Fri, 26 Jun 2020 09:45:31: 16000000 INFO @ Fri, 26 Jun 2020 09:45:35: 12000000 INFO @ Fri, 26 Jun 2020 09:45:36: 23000000 INFO @ Fri, 26 Jun 2020 09:45:38: 17000000 INFO @ Fri, 26 Jun 2020 09:45:39: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:45:39: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:45:39: #1 total tags in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:45:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:45:39: #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 09:45:40: #1 tags after filtering in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:45:40: #1 finished! INFO @ Fri, 26 Jun 2020 09:45:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:45:41: #2 number of paired peaks: 359 WARNING @ Fri, 26 Jun 2020 09:45:41: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Fri, 26 Jun 2020 09:45:41: start model_add_line... INFO @ Fri, 26 Jun 2020 09:45:41: start X-correlation... INFO @ Fri, 26 Jun 2020 09:45:41: end of X-cor INFO @ Fri, 26 Jun 2020 09:45:41: #2 finished! INFO @ Fri, 26 Jun 2020 09:45:41: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 09:45:41: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 26 Jun 2020 09:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05_model.r WARNING @ Fri, 26 Jun 2020 09:45:41: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:45:41: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 26 Jun 2020 09:45:41: #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 09:45:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:45:42: 13000000 INFO @ Fri, 26 Jun 2020 09:45:45: 18000000 INFO @ Fri, 26 Jun 2020 09:45:49: 14000000 INFO @ Fri, 26 Jun 2020 09:45:52: 19000000 INFO @ Fri, 26 Jun 2020 09:45:56: 15000000 INFO @ Fri, 26 Jun 2020 09:45:59: 20000000 INFO @ Fri, 26 Jun 2020 09:46:02: 16000000 INFO @ Fri, 26 Jun 2020 09:46:06: 21000000 INFO @ Fri, 26 Jun 2020 09:46:09: 17000000 INFO @ Fri, 26 Jun 2020 09:46:12: 22000000 INFO @ Fri, 26 Jun 2020 09:46:16: 18000000 INFO @ Fri, 26 Jun 2020 09:46:19: 23000000 INFO @ Fri, 26 Jun 2020 09:46:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:46:22: 19000000 INFO @ Fri, 26 Jun 2020 09:46:23: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:46:23: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:46:23: #1 total tags in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:46:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:46:23: #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 09:46:23: #1 tags after filtering in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:46:23: #1 finished! INFO @ Fri, 26 Jun 2020 09:46:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:46:25: #2 number of paired peaks: 359 WARNING @ Fri, 26 Jun 2020 09:46:25: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Fri, 26 Jun 2020 09:46:25: start model_add_line... INFO @ Fri, 26 Jun 2020 09:46:25: start X-correlation... INFO @ Fri, 26 Jun 2020 09:46:25: end of X-cor INFO @ Fri, 26 Jun 2020 09:46:25: #2 finished! INFO @ Fri, 26 Jun 2020 09:46:25: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 09:46:25: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 26 Jun 2020 09:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10_model.r WARNING @ Fri, 26 Jun 2020 09:46:25: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:46:25: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 26 Jun 2020 09:46:25: #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 09:46:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:46:29: 20000000 INFO @ Fri, 26 Jun 2020 09:46:35: 21000000 INFO @ Fri, 26 Jun 2020 09:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.05_summits.bed INFO @ Fri, 26 Jun 2020 09:46:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10662 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:46:41: 22000000 INFO @ Fri, 26 Jun 2020 09:46:47: 23000000 INFO @ Fri, 26 Jun 2020 09:46:50: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:46:50: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:46:50: #1 total tags in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:46:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:46:50: #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 09:46:51: #1 tags after filtering in treatment: 23502873 INFO @ Fri, 26 Jun 2020 09:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:46:51: #1 finished! INFO @ Fri, 26 Jun 2020 09:46:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:46:52: #2 number of paired peaks: 359 WARNING @ Fri, 26 Jun 2020 09:46:52: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Fri, 26 Jun 2020 09:46:52: start model_add_line... INFO @ Fri, 26 Jun 2020 09:46:53: start X-correlation... INFO @ Fri, 26 Jun 2020 09:46:53: end of X-cor INFO @ Fri, 26 Jun 2020 09:46:53: #2 finished! INFO @ Fri, 26 Jun 2020 09:46:53: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 09:46:53: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 26 Jun 2020 09:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20_model.r WARNING @ Fri, 26 Jun 2020 09:46:53: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:46:53: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 26 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 @ Fri, 26 Jun 2020 09:46:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:47:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.10_summits.bed INFO @ Fri, 26 Jun 2020 09:47:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4740 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:47:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750072/SRX750072.20_summits.bed INFO @ Fri, 26 Jun 2020 09:47:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2152 records, 4 fields): 5 millis CompletedMACS2peakCalling