Job ID = 6527791 SRX = SRX287602 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:18:09 prefetch.2.10.7: 1) Downloading 'SRR869745'... 2020-06-29T13:18:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:20:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:20:48 prefetch.2.10.7: 1) 'SRR869745' was downloaded successfully Read 21266404 spots for SRR869745/SRR869745.sra Written 21266404 spots for SRR869745/SRR869745.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: 00:07:30 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1402764 (6.60%) aligned 0 times 13365725 (62.85%) aligned exactly 1 time 6497915 (30.55%) aligned >1 times 93.40% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 3846008 / 19863640 = 0.1936 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 22:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.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 22:38:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:48: 1000000 INFO @ Mon, 29 Jun 2020 22:38:53: 2000000 INFO @ Mon, 29 Jun 2020 22:38:57: 3000000 INFO @ Mon, 29 Jun 2020 22:39:02: 4000000 INFO @ Mon, 29 Jun 2020 22:39:07: 5000000 INFO @ Mon, 29 Jun 2020 22:39:11: 6000000 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 22:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.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 22:39:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:39:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:39:16: 7000000 INFO @ Mon, 29 Jun 2020 22:39:18: 1000000 INFO @ Mon, 29 Jun 2020 22:39:21: 8000000 INFO @ Mon, 29 Jun 2020 22:39:23: 2000000 INFO @ Mon, 29 Jun 2020 22:39:25: 9000000 INFO @ Mon, 29 Jun 2020 22:39:28: 3000000 INFO @ Mon, 29 Jun 2020 22:39:30: 10000000 INFO @ Mon, 29 Jun 2020 22:39:33: 4000000 INFO @ Mon, 29 Jun 2020 22:39:35: 11000000 INFO @ Mon, 29 Jun 2020 22:39:37: 5000000 INFO @ Mon, 29 Jun 2020 22:39:39: 12000000 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 22:39:42: 6000000 INFO @ Mon, 29 Jun 2020 22:39:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.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 22:39:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:39:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:39:44: 13000000 INFO @ Mon, 29 Jun 2020 22:39:47: 7000000 INFO @ Mon, 29 Jun 2020 22:39:48: 1000000 INFO @ Mon, 29 Jun 2020 22:39:49: 14000000 INFO @ Mon, 29 Jun 2020 22:39:51: 8000000 INFO @ Mon, 29 Jun 2020 22:39:53: 2000000 INFO @ Mon, 29 Jun 2020 22:39:54: 15000000 INFO @ Mon, 29 Jun 2020 22:39:56: 9000000 INFO @ Mon, 29 Jun 2020 22:39:58: 3000000 INFO @ Mon, 29 Jun 2020 22:39:58: 16000000 INFO @ Mon, 29 Jun 2020 22:39:59: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:39:59: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:39:59: #1 total tags in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:39:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:39:59: #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 22:39:59: #1 tags after filtering in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:39:59: #1 finished! INFO @ Mon, 29 Jun 2020 22:39:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:40:00: #2 number of paired peaks: 239 WARNING @ Mon, 29 Jun 2020 22:40:00: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:00: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:00: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:00: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:00: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:00: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:40:00: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05_model.r WARNING @ Mon, 29 Jun 2020 22:40:00: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:00: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:40:00: #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 22:40:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:40:01: 10000000 INFO @ Mon, 29 Jun 2020 22:40:02: 4000000 INFO @ Mon, 29 Jun 2020 22:40:05: 11000000 INFO @ Mon, 29 Jun 2020 22:40:07: 5000000 INFO @ Mon, 29 Jun 2020 22:40:10: 12000000 INFO @ Mon, 29 Jun 2020 22:40:12: 6000000 INFO @ Mon, 29 Jun 2020 22:40:15: 13000000 INFO @ Mon, 29 Jun 2020 22:40:16: 7000000 INFO @ Mon, 29 Jun 2020 22:40:20: 14000000 INFO @ Mon, 29 Jun 2020 22:40:21: 8000000 INFO @ Mon, 29 Jun 2020 22:40:24: 15000000 INFO @ Mon, 29 Jun 2020 22:40:25: 9000000 INFO @ Mon, 29 Jun 2020 22:40:29: 16000000 INFO @ Mon, 29 Jun 2020 22:40:29: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:40:29: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:40:29: #1 total tags in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:40:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:40:29: #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 22:40:30: #1 tags after filtering in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:40:30: #1 finished! INFO @ Mon, 29 Jun 2020 22:40:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:40:30: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:40:30: 10000000 INFO @ Mon, 29 Jun 2020 22:40:31: #2 number of paired peaks: 239 WARNING @ Mon, 29 Jun 2020 22:40:31: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:31: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:31: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:31: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:31: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:31: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:40:31: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10_model.r WARNING @ Mon, 29 Jun 2020 22:40:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:31: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:40:31: #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 22:40:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:40:35: 11000000 INFO @ Mon, 29 Jun 2020 22:40:39: 12000000 INFO @ Mon, 29 Jun 2020 22:40:44: 13000000 INFO @ Mon, 29 Jun 2020 22:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.05_summits.bed INFO @ Mon, 29 Jun 2020 22:40:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2054 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:40:49: 14000000 INFO @ Mon, 29 Jun 2020 22:40:53: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:40:58: 16000000 INFO @ Mon, 29 Jun 2020 22:40:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:40:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:40:58: #1 total tags in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:40:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:40:58: #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 22:40:58: #1 tags after filtering in treatment: 16017632 INFO @ Mon, 29 Jun 2020 22:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:40:58: #1 finished! INFO @ Mon, 29 Jun 2020 22:40:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:40:59: #2 number of paired peaks: 239 WARNING @ Mon, 29 Jun 2020 22:40:59: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:59: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:59: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:59: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:59: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:59: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:40:59: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20_model.r WARNING @ Mon, 29 Jun 2020 22:40:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:59: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:40:59: #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 22:40:59: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:01: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.10_summits.bed INFO @ Mon, 29 Jun 2020 22:41:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1740 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:41:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287602/SRX287602.20_summits.bed INFO @ Mon, 29 Jun 2020 22:41:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 3 millis CompletedMACS2peakCalling