Job ID = 6458969 SRX = SRX5827837 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:02:01 prefetch.2.10.7: 1) Downloading 'SRR9051588'... 2020-06-21T13:02:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:02:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:02:54 prefetch.2.10.7: 'SRR9051588' is valid 2020-06-21T13:02:54 prefetch.2.10.7: 1) 'SRR9051588' was downloaded successfully 2020-06-21T13:02:54 prefetch.2.10.7: 'SRR9051588' has 0 unresolved dependencies Read 6626979 spots for SRR9051588/SRR9051588.sra Written 6626979 spots for SRR9051588/SRR9051588.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: 00:01:28 6626979 reads; of these: 6626979 (100.00%) were unpaired; of these: 2041477 (30.81%) aligned 0 times 3635606 (54.86%) aligned exactly 1 time 949896 (14.33%) aligned >1 times 69.19% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2592382 / 4585502 = 0.5653 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 22:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.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 22:06:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:21: 1000000 INFO @ Sun, 21 Jun 2020 22:06:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:06:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:06:28: #1 total tags in treatment: 1993120 INFO @ Sun, 21 Jun 2020 22:06:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:28: #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 22:06:28: #1 tags after filtering in treatment: 1993033 INFO @ Sun, 21 Jun 2020 22:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:29: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 22:06:29: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:29: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:06:29: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05_model.r WARNING @ Sun, 21 Jun 2020 22:06:29: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:29: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:06:29: #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 22:06:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.05_summits.bed INFO @ Sun, 21 Jun 2020 22:06:36: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (795 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 22:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.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 22:06:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:51: 1000000 INFO @ Sun, 21 Jun 2020 22:06:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:06:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:06:58: #1 total tags in treatment: 1993120 INFO @ Sun, 21 Jun 2020 22:06:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:58: #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 22:06:58: #1 tags after filtering in treatment: 1993033 INFO @ Sun, 21 Jun 2020 22:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:58: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 22:06:58: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:58: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:06:58: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:58: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:06:58: #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 22:06:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.10_summits.bed INFO @ Sun, 21 Jun 2020 22:07:05: Done! pass1 - making usageList (136 chroms): 0 millis pass2 - checking and writing primary data (279 records, 4 fields): 6 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 22:07:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.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 22:07:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:21: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:07:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:07:28: #1 total tags in treatment: 1993120 INFO @ Sun, 21 Jun 2020 22:07:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:28: #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 22:07:28: #1 tags after filtering in treatment: 1993033 INFO @ Sun, 21 Jun 2020 22:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:28: #2 number of paired peaks: 892 WARNING @ Sun, 21 Jun 2020 22:07:28: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Sun, 21 Jun 2020 22:07:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:28: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:07:28: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20_model.r WARNING @ Sun, 21 Jun 2020 22:07:28: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:28: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:07:28: #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 22:07:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:07:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827837/SRX5827837.20_summits.bed INFO @ Sun, 21 Jun 2020 22:07:35: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 3 millis CompletedMACS2peakCalling