Job ID = 6527806 SRX = SRX287693 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:25:08 prefetch.2.10.7: 1) Downloading 'SRR869881'... 2020-06-29T13:25:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:28:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:28:44 prefetch.2.10.7: 1) 'SRR869881' was downloaded successfully Read 23008083 spots for SRR869881/SRR869881.sra Written 23008083 spots for SRR869881/SRR869881.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: 00:08:37 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1291586 (5.61%) aligned 0 times 14514831 (63.09%) aligned exactly 1 time 7201666 (31.30%) aligned >1 times 94.39% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 3391465 / 21716497 = 0.1562 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 22:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.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 22:48:50: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:48:50: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:48:55: 1000000 INFO @ Mon, 29 Jun 2020 22:49:00: 2000000 INFO @ Mon, 29 Jun 2020 22:49:06: 3000000 INFO @ Mon, 29 Jun 2020 22:49:11: 4000000 INFO @ Mon, 29 Jun 2020 22:49:16: 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 22:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.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 22:49:20: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:49:20: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:49:22: 6000000 INFO @ Mon, 29 Jun 2020 22:49:25: 1000000 INFO @ Mon, 29 Jun 2020 22:49:27: 7000000 INFO @ Mon, 29 Jun 2020 22:49:29: 2000000 INFO @ Mon, 29 Jun 2020 22:49:32: 8000000 INFO @ Mon, 29 Jun 2020 22:49:34: 3000000 INFO @ Mon, 29 Jun 2020 22:49:38: 9000000 INFO @ Mon, 29 Jun 2020 22:49:39: 4000000 INFO @ Mon, 29 Jun 2020 22:49:43: 10000000 INFO @ Mon, 29 Jun 2020 22:49:44: 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 22:49:48: 11000000 INFO @ Mon, 29 Jun 2020 22:49:49: 6000000 INFO @ Mon, 29 Jun 2020 22:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.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 22:49:50: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:49:50: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:49:54: 7000000 INFO @ Mon, 29 Jun 2020 22:49:54: 12000000 INFO @ Mon, 29 Jun 2020 22:49:54: 1000000 INFO @ Mon, 29 Jun 2020 22:49:58: 8000000 INFO @ Mon, 29 Jun 2020 22:49:59: 13000000 INFO @ Mon, 29 Jun 2020 22:49:59: 2000000 INFO @ Mon, 29 Jun 2020 22:50:03: 9000000 INFO @ Mon, 29 Jun 2020 22:50:04: 3000000 INFO @ Mon, 29 Jun 2020 22:50:04: 14000000 INFO @ Mon, 29 Jun 2020 22:50:08: 10000000 INFO @ Mon, 29 Jun 2020 22:50:09: 4000000 INFO @ Mon, 29 Jun 2020 22:50:10: 15000000 INFO @ Mon, 29 Jun 2020 22:50:13: 11000000 INFO @ Mon, 29 Jun 2020 22:50:14: 5000000 INFO @ Mon, 29 Jun 2020 22:50:15: 16000000 INFO @ Mon, 29 Jun 2020 22:50:18: 12000000 INFO @ Mon, 29 Jun 2020 22:50:18: 6000000 INFO @ Mon, 29 Jun 2020 22:50:21: 17000000 INFO @ Mon, 29 Jun 2020 22:50:23: 13000000 INFO @ Mon, 29 Jun 2020 22:50:23: 7000000 INFO @ Mon, 29 Jun 2020 22:50:26: 18000000 INFO @ Mon, 29 Jun 2020 22:50:27: 14000000 INFO @ Mon, 29 Jun 2020 22:50:28: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:28: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:28: #1 total tags in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:50:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:28: #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 22:50:28: 8000000 INFO @ Mon, 29 Jun 2020 22:50:28: #1 tags after filtering in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:50:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:28: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:29: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 22:50:29: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:29: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:29: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:29: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:29: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:29: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:50:29: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 22:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05_model.r WARNING @ Mon, 29 Jun 2020 22:50:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:50:29: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 22:50:29: #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 22:50:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:32: 15000000 INFO @ Mon, 29 Jun 2020 22:50:33: 9000000 INFO @ Mon, 29 Jun 2020 22:50:37: 16000000 INFO @ Mon, 29 Jun 2020 22:50:38: 10000000 INFO @ Mon, 29 Jun 2020 22:50:42: 17000000 INFO @ Mon, 29 Jun 2020 22:50:42: 11000000 INFO @ Mon, 29 Jun 2020 22:50:47: 18000000 INFO @ Mon, 29 Jun 2020 22:50:47: 12000000 INFO @ Mon, 29 Jun 2020 22:50:48: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:48: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:48: #1 total tags in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:50:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:48: #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 22:50:49: #1 tags after filtering in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:49: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:50: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 22:50:50: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:50: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:50: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:50: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:50: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:50: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:50:50: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 22:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10_model.r WARNING @ Mon, 29 Jun 2020 22:50:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:50:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 22:50:50: #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 22:50:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:52: 13000000 INFO @ Mon, 29 Jun 2020 22:50:57: 14000000 INFO @ Mon, 29 Jun 2020 22:51:01: 15000000 INFO @ Mon, 29 Jun 2020 22:51:02: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:51:06: 16000000 INFO @ Mon, 29 Jun 2020 22:51:11: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:51:16: 18000000 INFO @ Mon, 29 Jun 2020 22:51:17: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:51:17: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:51:17: #1 total tags in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:51:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:51:17: #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 22:51:18: #1 tags after filtering in treatment: 18325032 INFO @ Mon, 29 Jun 2020 22:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:51:18: #1 finished! INFO @ Mon, 29 Jun 2020 22:51:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.05_summits.bed INFO @ Mon, 29 Jun 2020 22:51:19: Done! INFO @ Mon, 29 Jun 2020 22:51:19: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 22:51:19: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 22:51:19: start model_add_line... INFO @ Mon, 29 Jun 2020 22:51:19: start X-correlation... INFO @ Mon, 29 Jun 2020 22:51:19: end of X-cor INFO @ Mon, 29 Jun 2020 22:51:19: #2 finished! INFO @ Mon, 29 Jun 2020 22:51:19: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:51:19: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 22:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20_model.r pass1 - making usageList (14 chroms): 1 millis WARNING @ Mon, 29 Jun 2020 22:51:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:51:19: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 22:51:19: #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 22:51:19: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:51:19: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (2169 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:51:24: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.10_summits.bed INFO @ Mon, 29 Jun 2020 22:51:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1772 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:51:53: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287693/SRX287693.20_summits.bed INFO @ Mon, 29 Jun 2020 22:52:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1359 records, 4 fields): 3 millis CompletedMACS2peakCalling