Job ID = 6458429 SRX = SRX5226988 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:22:34 prefetch.2.10.7: 1) Downloading 'SRR8417903'... 2020-06-21T12:22:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:28:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:28:44 prefetch.2.10.7: 1) 'SRR8417903' was downloaded successfully 2020-06-21T12:28:44 prefetch.2.10.7: 'SRR8417903' has 0 unresolved dependencies Read 45544977 spots for SRR8417903/SRR8417903.sra Written 45544977 spots for SRR8417903/SRR8417903.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: 00:14:58 45544977 reads; of these: 45544977 (100.00%) were unpaired; of these: 3434074 (7.54%) aligned 0 times 31565515 (69.31%) aligned exactly 1 time 10545388 (23.15%) aligned >1 times 92.46% overall alignment rate Time searching: 00:14:59 Overall time: 00:14:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 8310194 / 42110903 = 0.1973 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 @ Sun, 21 Jun 2020 21:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.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 @ Sun, 21 Jun 2020 21:58:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:45: 1000000 INFO @ Sun, 21 Jun 2020 21:58:52: 2000000 INFO @ Sun, 21 Jun 2020 21:58:59: 3000000 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 @ Sun, 21 Jun 2020 21:59:06: 4000000 INFO @ Sun, 21 Jun 2020 21:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.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 @ Sun, 21 Jun 2020 21:59:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:14: 5000000 INFO @ Sun, 21 Jun 2020 21:59:15: 1000000 INFO @ Sun, 21 Jun 2020 21:59:22: 6000000 INFO @ Sun, 21 Jun 2020 21:59:23: 2000000 INFO @ Sun, 21 Jun 2020 21:59:30: 3000000 INFO @ Sun, 21 Jun 2020 21:59:30: 7000000 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 @ Sun, 21 Jun 2020 21:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.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 @ Sun, 21 Jun 2020 21:59:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:38: 4000000 INFO @ Sun, 21 Jun 2020 21:59:38: 8000000 INFO @ Sun, 21 Jun 2020 21:59:45: 1000000 INFO @ Sun, 21 Jun 2020 21:59:46: 5000000 INFO @ Sun, 21 Jun 2020 21:59:47: 9000000 INFO @ Sun, 21 Jun 2020 21:59:53: 2000000 INFO @ Sun, 21 Jun 2020 21:59:53: 6000000 INFO @ Sun, 21 Jun 2020 21:59:55: 10000000 INFO @ Sun, 21 Jun 2020 22:00:01: 3000000 INFO @ Sun, 21 Jun 2020 22:00:01: 7000000 INFO @ Sun, 21 Jun 2020 22:00:04: 11000000 INFO @ Sun, 21 Jun 2020 22:00:08: 4000000 INFO @ Sun, 21 Jun 2020 22:00:09: 8000000 INFO @ Sun, 21 Jun 2020 22:00:13: 12000000 INFO @ Sun, 21 Jun 2020 22:00:16: 5000000 INFO @ Sun, 21 Jun 2020 22:00:17: 9000000 INFO @ Sun, 21 Jun 2020 22:00:21: 13000000 INFO @ Sun, 21 Jun 2020 22:00:24: 6000000 INFO @ Sun, 21 Jun 2020 22:00:24: 10000000 INFO @ Sun, 21 Jun 2020 22:00:30: 14000000 INFO @ Sun, 21 Jun 2020 22:00:32: 7000000 INFO @ Sun, 21 Jun 2020 22:00:32: 11000000 INFO @ Sun, 21 Jun 2020 22:00:38: 15000000 INFO @ Sun, 21 Jun 2020 22:00:40: 8000000 INFO @ Sun, 21 Jun 2020 22:00:40: 12000000 INFO @ Sun, 21 Jun 2020 22:00:47: 16000000 INFO @ Sun, 21 Jun 2020 22:00:48: 9000000 INFO @ Sun, 21 Jun 2020 22:00:48: 13000000 INFO @ Sun, 21 Jun 2020 22:00:56: 10000000 INFO @ Sun, 21 Jun 2020 22:00:56: 14000000 INFO @ Sun, 21 Jun 2020 22:00:56: 17000000 INFO @ Sun, 21 Jun 2020 22:01:03: 11000000 INFO @ Sun, 21 Jun 2020 22:01:04: 15000000 INFO @ Sun, 21 Jun 2020 22:01:05: 18000000 INFO @ Sun, 21 Jun 2020 22:01:12: 12000000 INFO @ Sun, 21 Jun 2020 22:01:12: 16000000 INFO @ Sun, 21 Jun 2020 22:01:14: 19000000 INFO @ Sun, 21 Jun 2020 22:01:20: 13000000 INFO @ Sun, 21 Jun 2020 22:01:20: 17000000 INFO @ Sun, 21 Jun 2020 22:01:23: 20000000 INFO @ Sun, 21 Jun 2020 22:01:28: 14000000 INFO @ Sun, 21 Jun 2020 22:01:29: 18000000 INFO @ Sun, 21 Jun 2020 22:01:32: 21000000 INFO @ Sun, 21 Jun 2020 22:01:36: 15000000 INFO @ Sun, 21 Jun 2020 22:01:37: 19000000 INFO @ Sun, 21 Jun 2020 22:01:41: 22000000 INFO @ Sun, 21 Jun 2020 22:01:44: 16000000 INFO @ Sun, 21 Jun 2020 22:01:45: 20000000 INFO @ Sun, 21 Jun 2020 22:01:50: 23000000 INFO @ Sun, 21 Jun 2020 22:01:53: 17000000 INFO @ Sun, 21 Jun 2020 22:01:54: 21000000 INFO @ Sun, 21 Jun 2020 22:01:59: 24000000 INFO @ Sun, 21 Jun 2020 22:02:01: 18000000 INFO @ Sun, 21 Jun 2020 22:02:02: 22000000 INFO @ Sun, 21 Jun 2020 22:02:08: 25000000 INFO @ Sun, 21 Jun 2020 22:02:09: 19000000 INFO @ Sun, 21 Jun 2020 22:02:10: 23000000 INFO @ Sun, 21 Jun 2020 22:02:17: 26000000 INFO @ Sun, 21 Jun 2020 22:02:17: 20000000 INFO @ Sun, 21 Jun 2020 22:02:18: 24000000 INFO @ Sun, 21 Jun 2020 22:02:25: 21000000 INFO @ Sun, 21 Jun 2020 22:02:26: 27000000 INFO @ Sun, 21 Jun 2020 22:02:26: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:33: 22000000 INFO @ Sun, 21 Jun 2020 22:02:34: 26000000 INFO @ Sun, 21 Jun 2020 22:02:35: 28000000 INFO @ Sun, 21 Jun 2020 22:02:41: 23000000 INFO @ Sun, 21 Jun 2020 22:02:42: 27000000 INFO @ Sun, 21 Jun 2020 22:02:44: 29000000 INFO @ Sun, 21 Jun 2020 22:02:49: 24000000 INFO @ Sun, 21 Jun 2020 22:02:50: 28000000 INFO @ Sun, 21 Jun 2020 22:02:53: 30000000 INFO @ Sun, 21 Jun 2020 22:02:57: 25000000 INFO @ Sun, 21 Jun 2020 22:02:59: 29000000 INFO @ Sun, 21 Jun 2020 22:03:02: 31000000 INFO @ Sun, 21 Jun 2020 22:03:06: 26000000 INFO @ Sun, 21 Jun 2020 22:03:07: 30000000 INFO @ Sun, 21 Jun 2020 22:03:11: 32000000 INFO @ Sun, 21 Jun 2020 22:03:14: 27000000 INFO @ Sun, 21 Jun 2020 22:03:15: 31000000 INFO @ Sun, 21 Jun 2020 22:03:20: 33000000 INFO @ Sun, 21 Jun 2020 22:03:22: 28000000 INFO @ Sun, 21 Jun 2020 22:03:23: 32000000 INFO @ Sun, 21 Jun 2020 22:03:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:03:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:03:27: #1 total tags in treatment: 33800709 INFO @ Sun, 21 Jun 2020 22:03:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:03:28: #1 tags after filtering in treatment: 33800640 INFO @ Sun, 21 Jun 2020 22:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:30: #2 number of paired peaks: 334 WARNING @ Sun, 21 Jun 2020 22:03:30: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 21 Jun 2020 22:03:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:30: 29000000 INFO @ Sun, 21 Jun 2020 22:03:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:30: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:03:30: #2 alternative fragment length(s) may be 1,75 bps INFO @ Sun, 21 Jun 2020 22:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05_model.r WARNING @ Sun, 21 Jun 2020 22:03:30: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:30: #2 You may need to consider one of the other alternative d(s): 1,75 WARNING @ Sun, 21 Jun 2020 22:03:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:03:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:31: 33000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:03:37: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:03:37: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:03:37: #1 total tags in treatment: 33800709 INFO @ Sun, 21 Jun 2020 22:03:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:03:38: 30000000 INFO @ Sun, 21 Jun 2020 22:03:38: #1 tags after filtering in treatment: 33800640 INFO @ Sun, 21 Jun 2020 22:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:40: #2 number of paired peaks: 334 WARNING @ Sun, 21 Jun 2020 22:03:40: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 21 Jun 2020 22:03:40: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:40: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:40: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:40: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:40: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:03:40: #2 alternative fragment length(s) may be 1,75 bps INFO @ Sun, 21 Jun 2020 22:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10_model.r WARNING @ Sun, 21 Jun 2020 22:03:40: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:40: #2 You may need to consider one of the other alternative d(s): 1,75 WARNING @ Sun, 21 Jun 2020 22:03:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:03:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:45: 31000000 INFO @ Sun, 21 Jun 2020 22:03:52: 32000000 INFO @ Sun, 21 Jun 2020 22:03:58: 33000000 INFO @ Sun, 21 Jun 2020 22:04:04: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:04: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:04: #1 total tags in treatment: 33800709 INFO @ Sun, 21 Jun 2020 22:04:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:04:05: #1 tags after filtering in treatment: 33800640 INFO @ Sun, 21 Jun 2020 22:04:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:07: #2 number of paired peaks: 334 WARNING @ Sun, 21 Jun 2020 22:04:07: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:07: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:04:07: #2 alternative fragment length(s) may be 1,75 bps INFO @ Sun, 21 Jun 2020 22:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20_model.r WARNING @ Sun, 21 Jun 2020 22:04:07: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:07: #2 You may need to consider one of the other alternative d(s): 1,75 WARNING @ Sun, 21 Jun 2020 22:04:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:04:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:57: Done! pass1 - making usageList (513 chroms): 3 millis pass2 - checking and writing primary data (12103 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.10_summits.bed INFO @ Sun, 21 Jun 2020 22:05:09: Done! pass1 - making usageList (435 chroms): 1 millis pass2 - checking and writing primary data (4252 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226988/SRX5226988.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:33: Done! pass1 - making usageList (316 chroms): 1 millis pass2 - checking and writing primary data (1429 records, 4 fields): 10 millis CompletedMACS2peakCalling