Job ID = 6527638 SRX = SRX182777 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:03:50 prefetch.2.10.7: 1) Downloading 'SRR553570'... 2020-06-29T13:03:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:06:16 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:06:16 prefetch.2.10.7: 1) 'SRR553570' was downloaded successfully Read 29700681 spots for SRR553570/SRR553570.sra Written 29700681 spots for SRR553570/SRR553570.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: 00:13:43 29700681 reads; of these: 29700681 (100.00%) were unpaired; of these: 1850508 (6.23%) aligned 0 times 17478383 (58.85%) aligned exactly 1 time 10371790 (34.92%) aligned >1 times 93.77% overall alignment rate Time searching: 00:13:43 Overall time: 00:13:43 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 8 files... [bam_rmdupse_core] 5976899 / 27850173 = 0.2146 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 22:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.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 22:36:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:36:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:36:21: 1000000 INFO @ Mon, 29 Jun 2020 22:36:26: 2000000 INFO @ Mon, 29 Jun 2020 22:36:31: 3000000 INFO @ Mon, 29 Jun 2020 22:36:36: 4000000 INFO @ Mon, 29 Jun 2020 22:36:41: 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 @ Mon, 29 Jun 2020 22:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.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 22:36:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:36:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:36:46: 6000000 INFO @ Mon, 29 Jun 2020 22:36:51: 1000000 INFO @ Mon, 29 Jun 2020 22:36:52: 7000000 INFO @ Mon, 29 Jun 2020 22:36:56: 2000000 INFO @ Mon, 29 Jun 2020 22:36:58: 8000000 INFO @ Mon, 29 Jun 2020 22:37:01: 3000000 INFO @ Mon, 29 Jun 2020 22:37:03: 9000000 INFO @ Mon, 29 Jun 2020 22:37:07: 4000000 INFO @ Mon, 29 Jun 2020 22:37:09: 10000000 INFO @ Mon, 29 Jun 2020 22:37:12: 5000000 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 22:37:14: 11000000 INFO @ Mon, 29 Jun 2020 22:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.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 22:37:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:37:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:37:18: 6000000 INFO @ Mon, 29 Jun 2020 22:37:20: 12000000 INFO @ Mon, 29 Jun 2020 22:37:21: 1000000 INFO @ Mon, 29 Jun 2020 22:37:24: 7000000 INFO @ Mon, 29 Jun 2020 22:37:25: 13000000 INFO @ Mon, 29 Jun 2020 22:37:26: 2000000 INFO @ Mon, 29 Jun 2020 22:37:29: 8000000 INFO @ Mon, 29 Jun 2020 22:37:31: 14000000 INFO @ Mon, 29 Jun 2020 22:37:31: 3000000 INFO @ Mon, 29 Jun 2020 22:37:35: 9000000 INFO @ Mon, 29 Jun 2020 22:37:37: 15000000 INFO @ Mon, 29 Jun 2020 22:37:37: 4000000 INFO @ Mon, 29 Jun 2020 22:37:41: 10000000 INFO @ Mon, 29 Jun 2020 22:37:42: 16000000 INFO @ Mon, 29 Jun 2020 22:37:43: 5000000 INFO @ Mon, 29 Jun 2020 22:37:46: 11000000 INFO @ Mon, 29 Jun 2020 22:37:48: 6000000 INFO @ Mon, 29 Jun 2020 22:37:48: 17000000 INFO @ Mon, 29 Jun 2020 22:37:52: 12000000 INFO @ Mon, 29 Jun 2020 22:37:54: 18000000 INFO @ Mon, 29 Jun 2020 22:37:54: 7000000 INFO @ Mon, 29 Jun 2020 22:37:58: 13000000 INFO @ Mon, 29 Jun 2020 22:38:00: 19000000 INFO @ Mon, 29 Jun 2020 22:38:01: 8000000 INFO @ Mon, 29 Jun 2020 22:38:04: 14000000 INFO @ Mon, 29 Jun 2020 22:38:06: 20000000 INFO @ Mon, 29 Jun 2020 22:38:07: 9000000 INFO @ Mon, 29 Jun 2020 22:38:10: 15000000 INFO @ Mon, 29 Jun 2020 22:38:12: 21000000 INFO @ Mon, 29 Jun 2020 22:38:13: 10000000 INFO @ Mon, 29 Jun 2020 22:38:16: 16000000 INFO @ Mon, 29 Jun 2020 22:38:18: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:38:18: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:38:18: #1 total tags in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:38:18: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:38:18: #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 22:38:18: #1 tags after filtering in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:38:18: #1 finished! INFO @ Mon, 29 Jun 2020 22:38:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:38:20: 11000000 INFO @ Mon, 29 Jun 2020 22:38:20: #2 number of paired peaks: 187 WARNING @ Mon, 29 Jun 2020 22:38:20: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 29 Jun 2020 22:38:20: start model_add_line... INFO @ Mon, 29 Jun 2020 22:38:20: start X-correlation... INFO @ Mon, 29 Jun 2020 22:38:20: end of X-cor INFO @ Mon, 29 Jun 2020 22:38:20: #2 finished! INFO @ Mon, 29 Jun 2020 22:38:20: #2 predicted fragment length is 32 bps INFO @ Mon, 29 Jun 2020 22:38:20: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 29 Jun 2020 22:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05_model.r WARNING @ Mon, 29 Jun 2020 22:38:20: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:38:20: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 29 Jun 2020 22:38:20: #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 22:38:20: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:38:22: 17000000 INFO @ Mon, 29 Jun 2020 22:38:26: 12000000 INFO @ Mon, 29 Jun 2020 22:38:28: 18000000 INFO @ Mon, 29 Jun 2020 22:38:33: 13000000 INFO @ Mon, 29 Jun 2020 22:38:34: 19000000 INFO @ Mon, 29 Jun 2020 22:38:40: 14000000 INFO @ Mon, 29 Jun 2020 22:38:40: 20000000 INFO @ Mon, 29 Jun 2020 22:38:46: 21000000 INFO @ Mon, 29 Jun 2020 22:38:47: 15000000 INFO @ Mon, 29 Jun 2020 22:38:52: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:38:52: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:38:52: #1 total tags in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:38:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:38:52: #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 22:38:53: #1 tags after filtering in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:38:53: #1 finished! INFO @ Mon, 29 Jun 2020 22:38:53: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:38:54: #2 number of paired peaks: 187 WARNING @ Mon, 29 Jun 2020 22:38:54: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 29 Jun 2020 22:38:54: start model_add_line... INFO @ Mon, 29 Jun 2020 22:38:54: start X-correlation... INFO @ Mon, 29 Jun 2020 22:38:54: end of X-cor INFO @ Mon, 29 Jun 2020 22:38:54: #2 finished! INFO @ Mon, 29 Jun 2020 22:38:54: #2 predicted fragment length is 32 bps INFO @ Mon, 29 Jun 2020 22:38:54: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 29 Jun 2020 22:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10_model.r WARNING @ Mon, 29 Jun 2020 22:38:54: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:38:54: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 29 Jun 2020 22:38:54: #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 22:38:54: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:38:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:38:55: 16000000 INFO @ Mon, 29 Jun 2020 22:38:55: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:39:02: 17000000 INFO @ Mon, 29 Jun 2020 22:39:09: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.05_summits.bed INFO @ Mon, 29 Jun 2020 22:39:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2927 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:39:16: 19000000 INFO @ Mon, 29 Jun 2020 22:39:23: 20000000 INFO @ Mon, 29 Jun 2020 22:39:30: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:39:30: 21000000 INFO @ Mon, 29 Jun 2020 22:39:36: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:39:36: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:39:36: #1 total tags in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:39:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:39:36: #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 22:39:36: #1 tags after filtering in treatment: 21873274 INFO @ Mon, 29 Jun 2020 22:39:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:39:36: #1 finished! INFO @ Mon, 29 Jun 2020 22:39:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:39:38: #2 number of paired peaks: 187 WARNING @ Mon, 29 Jun 2020 22:39:38: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 29 Jun 2020 22:39:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:39:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:39:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:39:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:39:38: #2 predicted fragment length is 32 bps INFO @ Mon, 29 Jun 2020 22:39:38: #2 alternative fragment length(s) may be 32 bps INFO @ Mon, 29 Jun 2020 22:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20_model.r WARNING @ Mon, 29 Jun 2020 22:39:38: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:39:38: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Mon, 29 Jun 2020 22:39:38: #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 22:39:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:39:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.10_summits.bed INFO @ Mon, 29 Jun 2020 22:39:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:40:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX182777/SRX182777.20_summits.bed INFO @ Mon, 29 Jun 2020 22:40:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1282 records, 4 fields): 4 millis CompletedMACS2peakCalling