Job ID = 6457074 SRX = SRX4375837 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:24:24 prefetch.2.10.7: 1) Downloading 'SRR7506491'... 2020-06-21T11:24:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:58 prefetch.2.10.7: 'SRR7506491' is valid 2020-06-21T11:25:58 prefetch.2.10.7: 1) 'SRR7506491' was downloaded successfully Read 4451115 spots for SRR7506491/SRR7506491.sra Written 4451115 spots for SRR7506491/SRR7506491.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: 00:00:56 4451115 reads; of these: 4451115 (100.00%) were unpaired; of these: 1407249 (31.62%) aligned 0 times 2272147 (51.05%) aligned exactly 1 time 771719 (17.34%) aligned >1 times 68.38% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 288619 / 3043866 = 0.0948 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 20:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.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 20:28:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:38: 1000000 INFO @ Sun, 21 Jun 2020 20:28:44: 2000000 INFO @ Sun, 21 Jun 2020 20:28:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:49: #1 total tags in treatment: 2755247 INFO @ Sun, 21 Jun 2020 20:28:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:49: #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 20:28:49: #1 tags after filtering in treatment: 2754969 INFO @ Sun, 21 Jun 2020 20:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:49: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 20:28:49: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:49: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:28:49: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05_model.r WARNING @ Sun, 21 Jun 2020 20:28:49: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:49: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:28:49: #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 20:28:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.05_summits.bed INFO @ Sun, 21 Jun 2020 20:28:59: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 20:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.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 20:29:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:07: 1000000 INFO @ Sun, 21 Jun 2020 20:29:12: 2000000 INFO @ Sun, 21 Jun 2020 20:29:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:17: #1 total tags in treatment: 2755247 INFO @ Sun, 21 Jun 2020 20:29:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:17: #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 20:29:17: #1 tags after filtering in treatment: 2754969 INFO @ Sun, 21 Jun 2020 20:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:17: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 20:29:17: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:17: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:29:17: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10_model.r WARNING @ Sun, 21 Jun 2020 20:29:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:17: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:29:17: #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 20:29:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.10_summits.bed INFO @ Sun, 21 Jun 2020 20:29:27: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 20:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.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 20:29:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:37: 1000000 INFO @ Sun, 21 Jun 2020 20:29:42: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:47: #1 total tags in treatment: 2755247 INFO @ Sun, 21 Jun 2020 20:29:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:47: #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 20:29:47: #1 tags after filtering in treatment: 2754969 INFO @ Sun, 21 Jun 2020 20:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:47: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 20:29:47: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:47: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:29:47: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 20:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20_model.r WARNING @ Sun, 21 Jun 2020 20:29:47: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:47: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 20:29:47: #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 20:29:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:29:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375837/SRX4375837.20_summits.bed INFO @ Sun, 21 Jun 2020 20:29:57: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 3 millis CompletedMACS2peakCalling