Job ID = 6454030 SRX = SRX1794217 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:47 prefetch.2.10.7: 1) Downloading 'SRR3575249'... 2020-06-21T08:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:33 prefetch.2.10.7: 'SRR3575249' is valid 2020-06-21T08:42:33 prefetch.2.10.7: 1) 'SRR3575249' was downloaded successfully Read 8694064 spots for SRR3575249/SRR3575249.sra Written 8694064 spots for SRR3575249/SRR3575249.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: 00:02:29 8694064 reads; of these: 8694064 (100.00%) were unpaired; of these: 303302 (3.49%) aligned 0 times 6369157 (73.26%) aligned exactly 1 time 2021605 (23.25%) aligned >1 times 96.51% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 333460 / 8390762 = 0.0397 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 17:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.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 17:48:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:33: 1000000 INFO @ Sun, 21 Jun 2020 17:48:39: 2000000 INFO @ Sun, 21 Jun 2020 17:48:45: 3000000 INFO @ Sun, 21 Jun 2020 17:48:51: 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 @ Sun, 21 Jun 2020 17:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.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 17:48:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:57: 5000000 INFO @ Sun, 21 Jun 2020 17:49:04: 6000000 INFO @ Sun, 21 Jun 2020 17:49:05: 1000000 INFO @ Sun, 21 Jun 2020 17:49:12: 7000000 INFO @ Sun, 21 Jun 2020 17:49:13: 2000000 INFO @ Sun, 21 Jun 2020 17:49:20: 8000000 INFO @ Sun, 21 Jun 2020 17:49:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:20: #1 total tags in treatment: 8057302 INFO @ Sun, 21 Jun 2020 17:49:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:20: #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 17:49:21: #1 tags after filtering in treatment: 8057194 INFO @ Sun, 21 Jun 2020 17:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:21: 3000000 INFO @ Sun, 21 Jun 2020 17:49:21: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 17:49:21: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:21: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:49:21: #2 alternative fragment length(s) may be 4,56,162,589 bps INFO @ Sun, 21 Jun 2020 17:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05_model.r WARNING @ Sun, 21 Jun 2020 17:49:21: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:21: #2 You may need to consider one of the other alternative d(s): 4,56,162,589 WARNING @ Sun, 21 Jun 2020 17:49:21: #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 17:49:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:21: #3 Pre-compute pvalue-qvalue table... 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 17:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.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 17:49:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:28: 4000000 INFO @ Sun, 21 Jun 2020 17:49:36: 1000000 INFO @ Sun, 21 Jun 2020 17:49:36: 5000000 INFO @ Sun, 21 Jun 2020 17:49:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:44: 2000000 INFO @ Sun, 21 Jun 2020 17:49:44: 6000000 INFO @ Sun, 21 Jun 2020 17:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:49: Done! pass1 - making usageList (362 chroms): 0 millis pass2 - checking and writing primary data (1140 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:51: 3000000 INFO @ Sun, 21 Jun 2020 17:49:52: 7000000 INFO @ Sun, 21 Jun 2020 17:49:59: 4000000 INFO @ Sun, 21 Jun 2020 17:50:00: 8000000 INFO @ Sun, 21 Jun 2020 17:50:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:00: #1 total tags in treatment: 8057302 INFO @ Sun, 21 Jun 2020 17:50:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:00: #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 17:50:01: #1 tags after filtering in treatment: 8057194 INFO @ Sun, 21 Jun 2020 17:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:01: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 17:50:01: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 17:50:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:02: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:50:02: #2 alternative fragment length(s) may be 4,56,162,589 bps INFO @ Sun, 21 Jun 2020 17:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10_model.r WARNING @ Sun, 21 Jun 2020 17:50:02: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:02: #2 You may need to consider one of the other alternative d(s): 4,56,162,589 WARNING @ Sun, 21 Jun 2020 17:50:02: #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 17:50:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:06: 5000000 INFO @ Sun, 21 Jun 2020 17:50:13: 6000000 INFO @ Sun, 21 Jun 2020 17:50:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:21: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:28: 8000000 INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:28: Done! pass1 - making usageList (168 chroms): 1 millis pass2 - checking and writing primary data (472 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:28: #1 total tags in treatment: 8057302 INFO @ Sun, 21 Jun 2020 17:50:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:28: #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 17:50:28: #1 tags after filtering in treatment: 8057194 INFO @ Sun, 21 Jun 2020 17:50:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:29: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 17:50:29: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 17:50:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:29: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:50:29: #2 alternative fragment length(s) may be 4,56,162,589 bps INFO @ Sun, 21 Jun 2020 17:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20_model.r WARNING @ Sun, 21 Jun 2020 17:50:29: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:29: #2 You may need to consider one of the other alternative d(s): 4,56,162,589 WARNING @ Sun, 21 Jun 2020 17:50:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:50:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794217/SRX1794217.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:55: Done! pass1 - making usageList (87 chroms): 0 millis pass2 - checking and writing primary data (194 records, 4 fields): 4 millis CompletedMACS2peakCalling