Job ID = 6452650 SRX = SRX022746 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:51 prefetch.2.10.7: 1) Downloading 'SRR059125'... 2020-06-21T07:38:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:39:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:39:58 prefetch.2.10.7: 'SRR059125' is valid 2020-06-21T07:39:58 prefetch.2.10.7: 1) 'SRR059125' was downloaded successfully Read 9144494 spots for SRR059125/SRR059125.sra Written 9144494 spots for SRR059125/SRR059125.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:50 9144494 reads; of these: 9144494 (100.00%) were unpaired; of these: 1492037 (16.32%) aligned 0 times 5890954 (64.42%) aligned exactly 1 time 1761503 (19.26%) aligned >1 times 83.68% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 588297 / 7652457 = 0.0769 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 16:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.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 16:44:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:26: 1000000 INFO @ Sun, 21 Jun 2020 16:44:32: 2000000 INFO @ Sun, 21 Jun 2020 16:44:39: 3000000 INFO @ Sun, 21 Jun 2020 16:44:46: 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 16:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.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 16:44:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:53: 5000000 INFO @ Sun, 21 Jun 2020 16:44:56: 1000000 INFO @ Sun, 21 Jun 2020 16:45:01: 6000000 INFO @ Sun, 21 Jun 2020 16:45:03: 2000000 INFO @ Sun, 21 Jun 2020 16:45:09: 7000000 INFO @ Sun, 21 Jun 2020 16:45:09: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:09: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:09: #1 total tags in treatment: 7064160 INFO @ Sun, 21 Jun 2020 16:45:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:09: #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 16:45:10: #1 tags after filtering in treatment: 7064027 INFO @ Sun, 21 Jun 2020 16:45:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:10: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:10: 3000000 INFO @ Sun, 21 Jun 2020 16:45:10: #2 number of paired peaks: 806 WARNING @ Sun, 21 Jun 2020 16:45:10: Fewer paired peaks (806) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 806 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:10: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:10: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:10: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:10: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:10: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 16:45:10: #2 alternative fragment length(s) may be 4,41,549,592,594 bps INFO @ Sun, 21 Jun 2020 16:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05_model.r WARNING @ Sun, 21 Jun 2020 16:45:10: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:45:10: #2 You may need to consider one of the other alternative d(s): 4,41,549,592,594 WARNING @ Sun, 21 Jun 2020 16:45:10: #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 16:45:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:10: #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 16:45:16: 4000000 INFO @ Sun, 21 Jun 2020 16:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.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 16:45:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:45:23: 5000000 INFO @ Sun, 21 Jun 2020 16:45:26: 1000000 INFO @ Sun, 21 Jun 2020 16:45:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:31: 6000000 INFO @ Sun, 21 Jun 2020 16:45:34: 2000000 INFO @ Sun, 21 Jun 2020 16:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.05_summits.bed INFO @ Sun, 21 Jun 2020 16:45:36: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (1605 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:45:38: 7000000 INFO @ Sun, 21 Jun 2020 16:45:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:39: #1 total tags in treatment: 7064160 INFO @ Sun, 21 Jun 2020 16:45:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:39: #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 16:45:39: #1 tags after filtering in treatment: 7064027 INFO @ Sun, 21 Jun 2020 16:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:39: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:40: #2 number of paired peaks: 806 WARNING @ Sun, 21 Jun 2020 16:45:40: Fewer paired peaks (806) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 806 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:40: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:40: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 16:45:40: #2 alternative fragment length(s) may be 4,41,549,592,594 bps INFO @ Sun, 21 Jun 2020 16:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10_model.r WARNING @ Sun, 21 Jun 2020 16:45:40: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:45:40: #2 You may need to consider one of the other alternative d(s): 4,41,549,592,594 WARNING @ Sun, 21 Jun 2020 16:45:40: #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 16:45:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:41: 3000000 INFO @ Sun, 21 Jun 2020 16:45:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:45:55: 5000000 INFO @ Sun, 21 Jun 2020 16:45:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:02: 6000000 INFO @ Sun, 21 Jun 2020 16:46:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.10_summits.bed INFO @ Sun, 21 Jun 2020 16:46:05: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:46:09: 7000000 INFO @ Sun, 21 Jun 2020 16:46:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:46:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:46:10: #1 total tags in treatment: 7064160 INFO @ Sun, 21 Jun 2020 16:46:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:46:10: #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 16:46:10: #1 tags after filtering in treatment: 7064027 INFO @ Sun, 21 Jun 2020 16:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:46:10: #1 finished! INFO @ Sun, 21 Jun 2020 16:46:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:46:11: #2 number of paired peaks: 806 WARNING @ Sun, 21 Jun 2020 16:46:11: Fewer paired peaks (806) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 806 pairs to build model! INFO @ Sun, 21 Jun 2020 16:46:11: start model_add_line... INFO @ Sun, 21 Jun 2020 16:46:11: start X-correlation... INFO @ Sun, 21 Jun 2020 16:46:11: end of X-cor INFO @ Sun, 21 Jun 2020 16:46:11: #2 finished! INFO @ Sun, 21 Jun 2020 16:46:11: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 16:46:11: #2 alternative fragment length(s) may be 4,41,549,592,594 bps INFO @ Sun, 21 Jun 2020 16:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20_model.r WARNING @ Sun, 21 Jun 2020 16:46:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:46:11: #2 You may need to consider one of the other alternative d(s): 4,41,549,592,594 WARNING @ Sun, 21 Jun 2020 16:46:11: #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 16:46:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:46:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022746/SRX022746.20_summits.bed INFO @ Sun, 21 Jun 2020 16:46:36: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 5 millis CompletedMACS2peakCalling