Job ID = 6455741 SRX = SRX288035 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:11:21 prefetch.2.10.7: 1) Downloading 'SRR870224'... 2020-06-21T10:11:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:24 prefetch.2.10.7: 1) 'SRR870224' was downloaded successfully Read 17570684 spots for SRR870224/SRR870224.sra Written 17570684 spots for SRR870224/SRR870224.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: 00:05:24 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 1164942 (6.63%) aligned 0 times 11092379 (63.13%) aligned exactly 1 time 5313363 (30.24%) aligned >1 times 93.37% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3299018 / 16405742 = 0.2011 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 19:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.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 19:26:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:12: 1000000 INFO @ Sun, 21 Jun 2020 19:26:20: 2000000 INFO @ Sun, 21 Jun 2020 19:26:28: 3000000 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 19:26:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.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 19:26:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:36: 4000000 INFO @ Sun, 21 Jun 2020 19:26:42: 1000000 INFO @ Sun, 21 Jun 2020 19:26:44: 5000000 INFO @ Sun, 21 Jun 2020 19:26:49: 2000000 INFO @ Sun, 21 Jun 2020 19:26:53: 6000000 INFO @ Sun, 21 Jun 2020 19:26:57: 3000000 INFO @ Sun, 21 Jun 2020 19:27:01: 7000000 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 19:27:04: 4000000 INFO @ Sun, 21 Jun 2020 19:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.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 19:27:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:10: 8000000 INFO @ Sun, 21 Jun 2020 19:27:12: 5000000 INFO @ Sun, 21 Jun 2020 19:27:13: 1000000 INFO @ Sun, 21 Jun 2020 19:27:18: 9000000 INFO @ Sun, 21 Jun 2020 19:27:20: 6000000 INFO @ Sun, 21 Jun 2020 19:27:22: 2000000 INFO @ Sun, 21 Jun 2020 19:27:27: 10000000 INFO @ Sun, 21 Jun 2020 19:27:28: 7000000 INFO @ Sun, 21 Jun 2020 19:27:30: 3000000 INFO @ Sun, 21 Jun 2020 19:27:35: 8000000 INFO @ Sun, 21 Jun 2020 19:27:36: 11000000 INFO @ Sun, 21 Jun 2020 19:27:39: 4000000 INFO @ Sun, 21 Jun 2020 19:27:43: 9000000 INFO @ Sun, 21 Jun 2020 19:27:45: 12000000 INFO @ Sun, 21 Jun 2020 19:27:48: 5000000 INFO @ Sun, 21 Jun 2020 19:27:51: 10000000 INFO @ Sun, 21 Jun 2020 19:27:54: 13000000 INFO @ Sun, 21 Jun 2020 19:27:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:55: #1 total tags in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:27:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:55: #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 19:27:55: #1 tags after filtering in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:27:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:56: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:27:56: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:56: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:27:56: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:27:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05_model.r WARNING @ Sun, 21 Jun 2020 19:27:56: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:56: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:27:56: #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 19:27:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:56: 6000000 INFO @ Sun, 21 Jun 2020 19:27:59: 11000000 INFO @ Sun, 21 Jun 2020 19:28:05: 7000000 INFO @ Sun, 21 Jun 2020 19:28:07: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:14: 8000000 INFO @ Sun, 21 Jun 2020 19:28:15: 13000000 INFO @ Sun, 21 Jun 2020 19:28:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:16: #1 total tags in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:28:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:16: #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 19:28:16: #1 tags after filtering in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:17: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:28:17: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:18: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:28:18: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:18: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:18: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:28:18: #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 19:28:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:22: 9000000 INFO @ Sun, 21 Jun 2020 19:28:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:30: 10000000 INFO @ Sun, 21 Jun 2020 19:28:38: 11000000 INFO @ Sun, 21 Jun 2020 19:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:39: Done! pass1 - making usageList (596 chroms): 1 millis pass2 - checking and writing primary data (2324 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:45: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:28:53: 13000000 INFO @ Sun, 21 Jun 2020 19:28:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:54: #1 total tags in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:28:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:54: #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 19:28:55: #1 tags after filtering in treatment: 13106724 INFO @ Sun, 21 Jun 2020 19:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:56: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:28:56: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:56: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:28:56: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20_model.r WARNING @ Sun, 21 Jun 2020 19:28:56: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:56: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:28:56: #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 19:28:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:59: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288035/SRX288035.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:39: Done! pass1 - making usageList (302 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 11 millis CompletedMACS2peakCalling