Job ID = 6457102 SRX = SRX4375862 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:43 prefetch.2.10.7: 1) Downloading 'SRR7506516'... 2020-06-21T11:40:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:41:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:41:25 prefetch.2.10.7: 'SRR7506516' is valid 2020-06-21T11:41:25 prefetch.2.10.7: 1) 'SRR7506516' was downloaded successfully Read 2834045 spots for SRR7506516/SRR7506516.sra Written 2834045 spots for SRR7506516/SRR7506516.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: 00:00:35 2834045 reads; of these: 2834045 (100.00%) were unpaired; of these: 1126482 (39.75%) aligned 0 times 1275361 (45.00%) aligned exactly 1 time 432202 (15.25%) aligned >1 times 60.25% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 258673 / 1707563 = 0.1515 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 20:43:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.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 20:43:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:13: 1000000 INFO @ Sun, 21 Jun 2020 20:43:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:16: #1 total tags in treatment: 1448890 INFO @ Sun, 21 Jun 2020 20:43:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:16: #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 20:43:16: #1 tags after filtering in treatment: 1448526 INFO @ Sun, 21 Jun 2020 20:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:16: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 20:43:16: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 20:43:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:16: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:43:16: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05_model.r WARNING @ Sun, 21 Jun 2020 20:43:16: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:16: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:43:16: #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 20:43:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:22: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 11 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 20:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.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 20:43:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:43: 1000000 INFO @ Sun, 21 Jun 2020 20:43:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:46: #1 total tags in treatment: 1448890 INFO @ Sun, 21 Jun 2020 20:43:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:46: #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 20:43:46: #1 tags after filtering in treatment: 1448526 INFO @ Sun, 21 Jun 2020 20:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:46: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 20:43:46: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 20:43:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:46: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:43:46: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10_model.r WARNING @ Sun, 21 Jun 2020 20:43:46: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:46: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:43:46: #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 20:43:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:51: Done! pass1 - making usageList (109 chroms): 0 millis pass2 - checking and writing primary data (178 records, 4 fields): 4 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 20:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.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 20:44:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:13: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:16: #1 total tags in treatment: 1448890 INFO @ Sun, 21 Jun 2020 20:44:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:16: #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 20:44:16: #1 tags after filtering in treatment: 1448526 INFO @ Sun, 21 Jun 2020 20:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:16: #2 number of paired peaks: 896 WARNING @ Sun, 21 Jun 2020 20:44:16: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sun, 21 Jun 2020 20:44:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:16: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:44:16: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 20:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20_model.r WARNING @ Sun, 21 Jun 2020 20:44:16: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:44:16: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 20:44:16: #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 20:44:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375862/SRX4375862.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:21: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling