Job ID = 6497964 SRX = SRX287670 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:45:52 prefetch.2.10.7: 1) Downloading 'SRR869858'... 2020-06-25T23:45:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:47:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:47:17 prefetch.2.10.7: 'SRR869858' is valid 2020-06-25T23:47:17 prefetch.2.10.7: 1) 'SRR869858' was downloaded successfully Read 13389851 spots for SRR869858/SRR869858.sra Written 13389851 spots for SRR869858/SRR869858.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: 00:05:28 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 780883 (5.83%) aligned 0 times 8324610 (62.17%) aligned exactly 1 time 4284358 (32.00%) aligned >1 times 94.17% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 1578684 / 12608968 = 0.1252 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 @ Fri, 26 Jun 2020 08:58:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.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 @ Fri, 26 Jun 2020 08:58:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:58:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:58:08: 1000000 INFO @ Fri, 26 Jun 2020 08:58:14: 2000000 INFO @ Fri, 26 Jun 2020 08:58:20: 3000000 INFO @ Fri, 26 Jun 2020 08:58:25: 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 @ Fri, 26 Jun 2020 08:58:31: 5000000 INFO @ Fri, 26 Jun 2020 08:58:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.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 @ Fri, 26 Jun 2020 08:58:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:58:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:58:36: 6000000 INFO @ Fri, 26 Jun 2020 08:58:38: 1000000 INFO @ Fri, 26 Jun 2020 08:58:42: 7000000 INFO @ Fri, 26 Jun 2020 08:58:44: 2000000 INFO @ Fri, 26 Jun 2020 08:58:48: 8000000 INFO @ Fri, 26 Jun 2020 08:58:50: 3000000 INFO @ Fri, 26 Jun 2020 08:58:53: 9000000 INFO @ Fri, 26 Jun 2020 08:58:56: 4000000 INFO @ Fri, 26 Jun 2020 08:58:59: 10000000 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 @ Fri, 26 Jun 2020 08:59:02: 5000000 INFO @ Fri, 26 Jun 2020 08:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.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 @ Fri, 26 Jun 2020 08:59:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:59:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:59:05: 11000000 INFO @ Fri, 26 Jun 2020 08:59:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:59:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:59:05: #1 total tags in treatment: 11030284 INFO @ Fri, 26 Jun 2020 08:59:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:59:05: #1 tags after filtering in treatment: 11030284 INFO @ Fri, 26 Jun 2020 08:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:59:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:59:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:59:06: #2 number of paired peaks: 513 WARNING @ Fri, 26 Jun 2020 08:59:06: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Fri, 26 Jun 2020 08:59:06: start model_add_line... INFO @ Fri, 26 Jun 2020 08:59:06: start X-correlation... INFO @ Fri, 26 Jun 2020 08:59:06: end of X-cor INFO @ Fri, 26 Jun 2020 08:59:06: #2 finished! INFO @ Fri, 26 Jun 2020 08:59:06: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:59:06: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:59:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05_model.r WARNING @ Fri, 26 Jun 2020 08:59:06: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:59:06: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:59:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:59:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:59:07: 6000000 INFO @ Fri, 26 Jun 2020 08:59:08: 1000000 INFO @ Fri, 26 Jun 2020 08:59:13: 7000000 INFO @ Fri, 26 Jun 2020 08:59:14: 2000000 INFO @ Fri, 26 Jun 2020 08:59:19: 8000000 INFO @ Fri, 26 Jun 2020 08:59:20: 3000000 INFO @ Fri, 26 Jun 2020 08:59:24: 9000000 INFO @ Fri, 26 Jun 2020 08:59:25: 4000000 INFO @ Fri, 26 Jun 2020 08:59:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:59:30: 10000000 INFO @ Fri, 26 Jun 2020 08:59:32: 5000000 INFO @ Fri, 26 Jun 2020 08:59:36: 11000000 INFO @ Fri, 26 Jun 2020 08:59:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:59:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:59:36: #1 total tags in treatment: 11030284 INFO @ Fri, 26 Jun 2020 08:59:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:59:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:59:36: #1 tags after filtering in treatment: 11030284 INFO @ Fri, 26 Jun 2020 08:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:59:36: #1 finished! INFO @ Fri, 26 Jun 2020 08:59:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.05_summits.bed INFO @ Fri, 26 Jun 2020 08:59:37: Done! INFO @ Fri, 26 Jun 2020 08:59:37: #2 number of paired peaks: 513 WARNING @ Fri, 26 Jun 2020 08:59:37: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Fri, 26 Jun 2020 08:59:37: start model_add_line... INFO @ Fri, 26 Jun 2020 08:59:37: start X-correlation... INFO @ Fri, 26 Jun 2020 08:59:37: end of X-cor INFO @ Fri, 26 Jun 2020 08:59:37: #2 finished! INFO @ Fri, 26 Jun 2020 08:59:37: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:59:37: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10_model.r pass1 - making usageList (14 chroms): 1 millis WARNING @ Fri, 26 Jun 2020 08:59:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:59:37: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:59:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:59:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:59:37: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (2056 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:59:37: 6000000 INFO @ Fri, 26 Jun 2020 08:59:43: 7000000 INFO @ Fri, 26 Jun 2020 08:59:49: 8000000 INFO @ Fri, 26 Jun 2020 08:59:55: 9000000 INFO @ Fri, 26 Jun 2020 08:59:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:00:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:00:07: 11000000 INFO @ Fri, 26 Jun 2020 09:00:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:00:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:00:07: #1 total tags in treatment: 11030284 INFO @ Fri, 26 Jun 2020 09:00:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:00:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:00:07: #1 tags after filtering in treatment: 11030284 INFO @ Fri, 26 Jun 2020 09:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:00:07: #1 finished! INFO @ Fri, 26 Jun 2020 09:00:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:00:08: #2 number of paired peaks: 513 WARNING @ Fri, 26 Jun 2020 09:00:08: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Fri, 26 Jun 2020 09:00:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:00:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:00:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:00:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:00:08: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 09:00:08: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 09:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20_model.r WARNING @ Fri, 26 Jun 2020 09:00:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:00:08: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 09:00:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:00:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.10_summits.bed INFO @ Fri, 26 Jun 2020 09:00:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1776 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:00:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287670/SRX287670.20_summits.bed INFO @ Fri, 26 Jun 2020 09:00:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1356 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。