Job ID = 6458334 SRX = SRX5011080 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:18:37 prefetch.2.10.7: 1) Downloading 'SRR8191529'... 2020-06-21T12:18:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:21:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:21:56 prefetch.2.10.7: 1) 'SRR8191529' was downloaded successfully Read 25155474 spots for SRR8191529/SRR8191529.sra Written 25155474 spots for SRR8191529/SRR8191529.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: 00:06:04 25155474 reads; of these: 25155474 (100.00%) were unpaired; of these: 3694796 (14.69%) aligned 0 times 16316611 (64.86%) aligned exactly 1 time 5144067 (20.45%) aligned >1 times 85.31% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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 12 files... [bam_rmdupse_core] 7418052 / 21460678 = 0.3457 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 21:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.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 21:33:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:39: 1000000 INFO @ Sun, 21 Jun 2020 21:33:45: 2000000 INFO @ Sun, 21 Jun 2020 21:33:51: 3000000 INFO @ Sun, 21 Jun 2020 21:33:56: 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 21:34:02: 5000000 INFO @ Sun, 21 Jun 2020 21:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.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 21:34:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:08: 1000000 INFO @ Sun, 21 Jun 2020 21:34:09: 6000000 INFO @ Sun, 21 Jun 2020 21:34:14: 2000000 INFO @ Sun, 21 Jun 2020 21:34:15: 7000000 INFO @ Sun, 21 Jun 2020 21:34:20: 3000000 INFO @ Sun, 21 Jun 2020 21:34:21: 8000000 INFO @ Sun, 21 Jun 2020 21:34:26: 4000000 INFO @ Sun, 21 Jun 2020 21:34:28: 9000000 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 21:34:32: 5000000 INFO @ Sun, 21 Jun 2020 21:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.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 21:34:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:34: 10000000 INFO @ Sun, 21 Jun 2020 21:34:38: 6000000 INFO @ Sun, 21 Jun 2020 21:34:39: 1000000 INFO @ Sun, 21 Jun 2020 21:34:41: 11000000 INFO @ Sun, 21 Jun 2020 21:34:44: 7000000 INFO @ Sun, 21 Jun 2020 21:34:46: 2000000 INFO @ Sun, 21 Jun 2020 21:34:47: 12000000 INFO @ Sun, 21 Jun 2020 21:34:50: 8000000 INFO @ Sun, 21 Jun 2020 21:34:53: 3000000 INFO @ Sun, 21 Jun 2020 21:34:54: 13000000 INFO @ Sun, 21 Jun 2020 21:34:56: 9000000 INFO @ Sun, 21 Jun 2020 21:34:59: 4000000 INFO @ Sun, 21 Jun 2020 21:35:00: 14000000 INFO @ Sun, 21 Jun 2020 21:35:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:01: #1 total tags in treatment: 14042626 INFO @ Sun, 21 Jun 2020 21:35:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:01: #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 21:35:01: #1 tags after filtering in treatment: 14042559 INFO @ Sun, 21 Jun 2020 21:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:01: 10000000 INFO @ Sun, 21 Jun 2020 21:35:02: #2 number of paired peaks: 914 WARNING @ Sun, 21 Jun 2020 21:35:02: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Sun, 21 Jun 2020 21:35:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:02: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:35:02: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 21:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05_model.r WARNING @ Sun, 21 Jun 2020 21:35:02: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:02: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Sun, 21 Jun 2020 21:35:02: #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 21:35:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:06: 5000000 INFO @ Sun, 21 Jun 2020 21:35:07: 11000000 INFO @ Sun, 21 Jun 2020 21:35:13: 6000000 INFO @ Sun, 21 Jun 2020 21:35:13: 12000000 INFO @ Sun, 21 Jun 2020 21:35:19: 13000000 INFO @ Sun, 21 Jun 2020 21:35:20: 7000000 INFO @ Sun, 21 Jun 2020 21:35:25: 14000000 INFO @ Sun, 21 Jun 2020 21:35:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:25: #1 total tags in treatment: 14042626 INFO @ Sun, 21 Jun 2020 21:35:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:25: #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 21:35:26: #1 tags after filtering in treatment: 14042559 INFO @ Sun, 21 Jun 2020 21:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:26: 8000000 INFO @ Sun, 21 Jun 2020 21:35:27: #2 number of paired peaks: 914 WARNING @ Sun, 21 Jun 2020 21:35:27: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Sun, 21 Jun 2020 21:35:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:27: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:35:27: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 21:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10_model.r WARNING @ Sun, 21 Jun 2020 21:35:27: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:27: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Sun, 21 Jun 2020 21:35:27: #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 21:35:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:39: 10000000 INFO @ Sun, 21 Jun 2020 21:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:44: Done! pass1 - making usageList (670 chroms): 2 millis pass2 - checking and writing primary data (3720 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:45: 11000000 INFO @ Sun, 21 Jun 2020 21:35:51: 12000000 INFO @ Sun, 21 Jun 2020 21:35:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:57: 13000000 INFO @ Sun, 21 Jun 2020 21:36:03: 14000000 INFO @ Sun, 21 Jun 2020 21:36:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:03: #1 total tags in treatment: 14042626 INFO @ Sun, 21 Jun 2020 21:36:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:03: #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 21:36:04: #1 tags after filtering in treatment: 14042559 INFO @ Sun, 21 Jun 2020 21:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:04: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:05: #2 number of paired peaks: 914 WARNING @ Sun, 21 Jun 2020 21:36:05: Fewer paired peaks (914) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 914 pairs to build model! INFO @ Sun, 21 Jun 2020 21:36:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:05: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:36:05: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 21:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20_model.r WARNING @ Sun, 21 Jun 2020 21:36:05: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:05: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Sun, 21 Jun 2020 21:36:05: #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 21:36:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:10: Done! pass1 - making usageList (454 chroms): 1 millis pass2 - checking and writing primary data (1969 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011080/SRX5011080.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:47: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 8 millis CompletedMACS2peakCalling