Job ID = 6452642 SRX = SRX020699 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:15 prefetch.2.10.7: 1) Downloading 'SRR060780'... 2020-06-21T07:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:57:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:57:53 prefetch.2.10.7: 1) 'SRR060780' was downloaded successfully Read 20118269 spots for SRR060780/SRR060780.sra Written 20118269 spots for SRR060780/SRR060780.sra 2020-06-21T07:59:02 prefetch.2.10.7: 1) Downloading 'SRR060781'... 2020-06-21T07:59:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:59:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:59:54 prefetch.2.10.7: 'SRR060781' is valid 2020-06-21T07:59:54 prefetch.2.10.7: 1) 'SRR060781' was downloaded successfully Read 9541597 spots for SRR060781/SRR060781.sra Written 9541597 spots for SRR060781/SRR060781.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: 00:04:10 29659866 reads; of these: 29659866 (100.00%) were unpaired; of these: 15463661 (52.14%) aligned 0 times 10853150 (36.59%) aligned exactly 1 time 3343055 (11.27%) aligned >1 times 47.86% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2560297 / 14196205 = 0.1804 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 @ Sun, 21 Jun 2020 17:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.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 @ Sun, 21 Jun 2020 17:07:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:58: 1000000 INFO @ Sun, 21 Jun 2020 17:08:03: 2000000 INFO @ Sun, 21 Jun 2020 17:08:08: 3000000 INFO @ Sun, 21 Jun 2020 17:08:13: 4000000 INFO @ Sun, 21 Jun 2020 17:08:18: 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 @ Sun, 21 Jun 2020 17:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.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 @ Sun, 21 Jun 2020 17:08:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:23: 6000000 INFO @ Sun, 21 Jun 2020 17:08:29: 7000000 INFO @ Sun, 21 Jun 2020 17:08:29: 1000000 INFO @ Sun, 21 Jun 2020 17:08:34: 8000000 INFO @ Sun, 21 Jun 2020 17:08:35: 2000000 INFO @ Sun, 21 Jun 2020 17:08:39: 9000000 INFO @ Sun, 21 Jun 2020 17:08:41: 3000000 INFO @ Sun, 21 Jun 2020 17:08:45: 10000000 INFO @ Sun, 21 Jun 2020 17:08:48: 4000000 INFO @ Sun, 21 Jun 2020 17:08:51: 11000000 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 @ Sun, 21 Jun 2020 17:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.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 @ Sun, 21 Jun 2020 17:08:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:54: 5000000 INFO @ Sun, 21 Jun 2020 17:08:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:55: #1 total tags in treatment: 11635908 INFO @ Sun, 21 Jun 2020 17:08:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:08:55: #1 tags after filtering in treatment: 11635906 INFO @ Sun, 21 Jun 2020 17:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:56: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:08:56: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:08:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:56: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:08:56: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 17:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05_model.r WARNING @ Sun, 21 Jun 2020 17:08:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:08:56: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 17:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:08:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:08:59: 1000000 INFO @ Sun, 21 Jun 2020 17:09:00: 6000000 INFO @ Sun, 21 Jun 2020 17:09:05: 2000000 INFO @ Sun, 21 Jun 2020 17:09:06: 7000000 INFO @ Sun, 21 Jun 2020 17:09:10: 3000000 INFO @ Sun, 21 Jun 2020 17:09:12: 8000000 INFO @ Sun, 21 Jun 2020 17:09:16: 4000000 INFO @ Sun, 21 Jun 2020 17:09:18: 9000000 INFO @ Sun, 21 Jun 2020 17:09:22: 5000000 INFO @ Sun, 21 Jun 2020 17:09:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:24: 10000000 INFO @ Sun, 21 Jun 2020 17:09:27: 6000000 INFO @ Sun, 21 Jun 2020 17:09:30: 11000000 INFO @ Sun, 21 Jun 2020 17:09:33: 7000000 INFO @ Sun, 21 Jun 2020 17:09:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:34: #1 total tags in treatment: 11635908 INFO @ Sun, 21 Jun 2020 17:09:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:09:34: #1 tags after filtering in treatment: 11635906 INFO @ Sun, 21 Jun 2020 17:09:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.05_summits.bed INFO @ Sun, 21 Jun 2020 17:09:35: Done! INFO @ Sun, 21 Jun 2020 17:09:35: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:09:35: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:35: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:09:35: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 17:09:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10_model.r WARNING @ Sun, 21 Jun 2020 17:09:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:35: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 17:09:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:09:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:35: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (562 chroms): 2 millis pass2 - checking and writing primary data (7486 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:38: 8000000 INFO @ Sun, 21 Jun 2020 17:09:43: 9000000 INFO @ Sun, 21 Jun 2020 17:09:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:09:54: 11000000 INFO @ Sun, 21 Jun 2020 17:09:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:57: #1 total tags in treatment: 11635908 INFO @ Sun, 21 Jun 2020 17:09:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:09:58: #1 tags after filtering in treatment: 11635906 INFO @ Sun, 21 Jun 2020 17:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:59: #2 number of paired peaks: 467 WARNING @ Sun, 21 Jun 2020 17:09:59: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:59: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:09:59: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 17:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20_model.r WARNING @ Sun, 21 Jun 2020 17:09:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:59: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 17:09:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:09:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:12: Done! pass1 - making usageList (258 chroms): 2 millis pass2 - checking and writing primary data (2367 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX020699/SRX020699.20_summits.bed INFO @ Sun, 21 Jun 2020 17:10:36: Done! pass1 - making usageList (99 chroms): 0 millis pass2 - checking and writing primary data (416 records, 4 fields): 6 millis CompletedMACS2peakCalling