Job ID = 6527426 SRX = ERX1266828 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:34:57 prefetch.2.10.7: 1) Downloading 'ERR1193512'... 2020-06-29T12:34:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:36:47 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:36:48 prefetch.2.10.7: 'ERR1193512' is valid 2020-06-29T12:36:48 prefetch.2.10.7: 1) 'ERR1193512' was downloaded successfully Read 14618454 spots for ERR1193512/ERR1193512.sra Written 14618454 spots for ERR1193512/ERR1193512.sra 2020-06-29T12:37:38 prefetch.2.10.7: 1) Downloading 'ERR1193515'... 2020-06-29T12:37:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:39:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:39:38 prefetch.2.10.7: 'ERR1193515' is valid 2020-06-29T12:39:38 prefetch.2.10.7: 1) 'ERR1193515' was downloaded successfully Read 14222718 spots for ERR1193515/ERR1193515.sra Written 14222718 spots for ERR1193515/ERR1193515.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: 00:09:25 28841172 reads; of these: 28841172 (100.00%) were unpaired; of these: 3633699 (12.60%) aligned 0 times 16916608 (58.65%) aligned exactly 1 time 8290865 (28.75%) aligned >1 times 87.40% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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 12 files... [bam_rmdupse_core] 5008003 / 25207473 = 0.1987 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 @ Mon, 29 Jun 2020 22:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.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 @ Mon, 29 Jun 2020 22:02:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:17: 1000000 INFO @ Mon, 29 Jun 2020 22:02:23: 2000000 INFO @ Mon, 29 Jun 2020 22:02:30: 3000000 INFO @ Mon, 29 Jun 2020 22:02:37: 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 @ Mon, 29 Jun 2020 22:02:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.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 @ Mon, 29 Jun 2020 22:02:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:44: 5000000 INFO @ Mon, 29 Jun 2020 22:02:46: 1000000 INFO @ Mon, 29 Jun 2020 22:02:51: 6000000 INFO @ Mon, 29 Jun 2020 22:02:52: 2000000 INFO @ Mon, 29 Jun 2020 22:02:58: 3000000 INFO @ Mon, 29 Jun 2020 22:02:59: 7000000 INFO @ Mon, 29 Jun 2020 22:03:05: 4000000 INFO @ Mon, 29 Jun 2020 22:03:06: 8000000 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 @ Mon, 29 Jun 2020 22:03:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.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 @ Mon, 29 Jun 2020 22:03:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:03:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:03:11: 5000000 INFO @ Mon, 29 Jun 2020 22:03:14: 9000000 INFO @ Mon, 29 Jun 2020 22:03:16: 1000000 INFO @ Mon, 29 Jun 2020 22:03:17: 6000000 INFO @ Mon, 29 Jun 2020 22:03:21: 10000000 INFO @ Mon, 29 Jun 2020 22:03:22: 2000000 INFO @ Mon, 29 Jun 2020 22:03:24: 7000000 INFO @ Mon, 29 Jun 2020 22:03:28: 11000000 INFO @ Mon, 29 Jun 2020 22:03:29: 3000000 INFO @ Mon, 29 Jun 2020 22:03:30: 8000000 INFO @ Mon, 29 Jun 2020 22:03:35: 4000000 INFO @ Mon, 29 Jun 2020 22:03:36: 12000000 INFO @ Mon, 29 Jun 2020 22:03:37: 9000000 INFO @ Mon, 29 Jun 2020 22:03:41: 5000000 INFO @ Mon, 29 Jun 2020 22:03:43: 10000000 INFO @ Mon, 29 Jun 2020 22:03:43: 13000000 INFO @ Mon, 29 Jun 2020 22:03:48: 6000000 INFO @ Mon, 29 Jun 2020 22:03:50: 11000000 INFO @ Mon, 29 Jun 2020 22:03:51: 14000000 INFO @ Mon, 29 Jun 2020 22:03:55: 7000000 INFO @ Mon, 29 Jun 2020 22:03:56: 12000000 INFO @ Mon, 29 Jun 2020 22:03:58: 15000000 INFO @ Mon, 29 Jun 2020 22:04:01: 8000000 INFO @ Mon, 29 Jun 2020 22:04:03: 13000000 INFO @ Mon, 29 Jun 2020 22:04:06: 16000000 INFO @ Mon, 29 Jun 2020 22:04:08: 9000000 INFO @ Mon, 29 Jun 2020 22:04:10: 14000000 INFO @ Mon, 29 Jun 2020 22:04:13: 17000000 INFO @ Mon, 29 Jun 2020 22:04:14: 10000000 INFO @ Mon, 29 Jun 2020 22:04:16: 15000000 INFO @ Mon, 29 Jun 2020 22:04:21: 18000000 INFO @ Mon, 29 Jun 2020 22:04:21: 11000000 INFO @ Mon, 29 Jun 2020 22:04:23: 16000000 INFO @ Mon, 29 Jun 2020 22:04:28: 12000000 INFO @ Mon, 29 Jun 2020 22:04:29: 19000000 INFO @ Mon, 29 Jun 2020 22:04:30: 17000000 INFO @ Mon, 29 Jun 2020 22:04:34: 13000000 INFO @ Mon, 29 Jun 2020 22:04:36: 20000000 INFO @ Mon, 29 Jun 2020 22:04:37: 18000000 INFO @ Mon, 29 Jun 2020 22:04:38: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:04:38: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:04:38: #1 total tags in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:04:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:04:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:04:38: #1 tags after filtering in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:04:38: #1 finished! INFO @ Mon, 29 Jun 2020 22:04:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:04:40: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 22:04:40: 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 @ Mon, 29 Jun 2020 22:04:40: start model_add_line... INFO @ Mon, 29 Jun 2020 22:04:40: start X-correlation... INFO @ Mon, 29 Jun 2020 22:04:40: end of X-cor INFO @ Mon, 29 Jun 2020 22:04:40: #2 finished! INFO @ Mon, 29 Jun 2020 22:04:40: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:04:40: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 29 Jun 2020 22:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05_model.r WARNING @ Mon, 29 Jun 2020 22:04:40: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:04:40: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 29 Jun 2020 22:04:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:04:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:04:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:04:41: 14000000 INFO @ Mon, 29 Jun 2020 22:04:43: 19000000 INFO @ Mon, 29 Jun 2020 22:04:47: 15000000 INFO @ Mon, 29 Jun 2020 22:04:50: 20000000 INFO @ Mon, 29 Jun 2020 22:04:51: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:04:51: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:04:51: #1 total tags in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:04:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:04:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:04:52: #1 tags after filtering in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:04:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:04:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:04:53: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 22:04:53: 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 @ Mon, 29 Jun 2020 22:04:53: start model_add_line... INFO @ Mon, 29 Jun 2020 22:04:53: start X-correlation... INFO @ Mon, 29 Jun 2020 22:04:53: end of X-cor INFO @ Mon, 29 Jun 2020 22:04:53: #2 finished! INFO @ Mon, 29 Jun 2020 22:04:53: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:04:53: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 29 Jun 2020 22:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10_model.r WARNING @ Mon, 29 Jun 2020 22:04:53: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:04:53: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 29 Jun 2020 22:04:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:04:53: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:04:54: 16000000 INFO @ Mon, 29 Jun 2020 22:05:00: 17000000 INFO @ Mon, 29 Jun 2020 22:05:06: 18000000 INFO @ Mon, 29 Jun 2020 22:05:12: 19000000 INFO @ Mon, 29 Jun 2020 22:05:18: 20000000 INFO @ Mon, 29 Jun 2020 22:05:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:05:19: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:05:19: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:05:19: #1 total tags in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:05:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:05:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:05:20: #1 tags after filtering in treatment: 20199470 INFO @ Mon, 29 Jun 2020 22:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:05:20: #1 finished! INFO @ Mon, 29 Jun 2020 22:05:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:05:21: #2 number of paired peaks: 139 WARNING @ Mon, 29 Jun 2020 22:05:21: 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 @ Mon, 29 Jun 2020 22:05:21: start model_add_line... INFO @ Mon, 29 Jun 2020 22:05:21: start X-correlation... INFO @ Mon, 29 Jun 2020 22:05:21: end of X-cor INFO @ Mon, 29 Jun 2020 22:05:21: #2 finished! INFO @ Mon, 29 Jun 2020 22:05:21: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:05:21: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 29 Jun 2020 22:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20_model.r WARNING @ Mon, 29 Jun 2020 22:05:21: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:05:21: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 29 Jun 2020 22:05:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:05:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:05:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:05:33: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.05_summits.bed INFO @ Mon, 29 Jun 2020 22:05:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1857 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:05:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:05:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:05:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.10_summits.bed INFO @ Mon, 29 Jun 2020 22:05:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1535 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:06:01: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266828/ERX1266828.20_summits.bed INFO @ Mon, 29 Jun 2020 22:06:21: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1123 records, 4 fields): 2 millis CompletedMACS2peakCalling