Job ID = 6459495 SRX = SRX6827676 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:20:50 prefetch.2.10.7: 1) Downloading 'SRR10095456'... 2020-06-21T13:20:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:24:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:24:45 prefetch.2.10.7: 1) 'SRR10095456' was downloaded successfully Read 25371043 spots for SRR10095456/SRR10095456.sra Written 25371043 spots for SRR10095456/SRR10095456.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: 00:07:26 25371043 reads; of these: 25371043 (100.00%) were unpaired; of these: 1015864 (4.00%) aligned 0 times 16892910 (66.58%) aligned exactly 1 time 7462269 (29.41%) aligned >1 times 96.00% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 5457572 / 24355179 = 0.2241 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 22:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.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 22:38:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:42: 1000000 INFO @ Sun, 21 Jun 2020 22:38:48: 2000000 INFO @ Sun, 21 Jun 2020 22:38:53: 3000000 INFO @ Sun, 21 Jun 2020 22:38:59: 4000000 INFO @ Sun, 21 Jun 2020 22:39:04: 5000000 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 22:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.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 22:39:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:10: 6000000 INFO @ Sun, 21 Jun 2020 22:39:13: 1000000 INFO @ Sun, 21 Jun 2020 22:39:16: 7000000 INFO @ Sun, 21 Jun 2020 22:39:18: 2000000 INFO @ Sun, 21 Jun 2020 22:39:21: 8000000 INFO @ Sun, 21 Jun 2020 22:39:24: 3000000 INFO @ Sun, 21 Jun 2020 22:39:27: 9000000 INFO @ Sun, 21 Jun 2020 22:39:30: 4000000 INFO @ Sun, 21 Jun 2020 22:39:32: 10000000 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 22:39:35: 5000000 INFO @ Sun, 21 Jun 2020 22:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.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 22:39:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:38: 11000000 INFO @ Sun, 21 Jun 2020 22:39:41: 6000000 INFO @ Sun, 21 Jun 2020 22:39:43: 1000000 INFO @ Sun, 21 Jun 2020 22:39:44: 12000000 INFO @ Sun, 21 Jun 2020 22:39:47: 7000000 INFO @ Sun, 21 Jun 2020 22:39:48: 2000000 INFO @ Sun, 21 Jun 2020 22:39:50: 13000000 INFO @ Sun, 21 Jun 2020 22:39:53: 8000000 INFO @ Sun, 21 Jun 2020 22:39:54: 3000000 INFO @ Sun, 21 Jun 2020 22:39:55: 14000000 INFO @ Sun, 21 Jun 2020 22:39:58: 9000000 INFO @ Sun, 21 Jun 2020 22:40:00: 4000000 INFO @ Sun, 21 Jun 2020 22:40:01: 15000000 INFO @ Sun, 21 Jun 2020 22:40:04: 10000000 INFO @ Sun, 21 Jun 2020 22:40:06: 5000000 INFO @ Sun, 21 Jun 2020 22:40:07: 16000000 INFO @ Sun, 21 Jun 2020 22:40:10: 11000000 INFO @ Sun, 21 Jun 2020 22:40:11: 6000000 INFO @ Sun, 21 Jun 2020 22:40:13: 17000000 INFO @ Sun, 21 Jun 2020 22:40:16: 12000000 INFO @ Sun, 21 Jun 2020 22:40:17: 7000000 INFO @ Sun, 21 Jun 2020 22:40:18: 18000000 INFO @ Sun, 21 Jun 2020 22:40:21: 13000000 INFO @ Sun, 21 Jun 2020 22:40:23: 8000000 INFO @ Sun, 21 Jun 2020 22:40:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:40:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:40:24: #1 total tags in treatment: 18897607 INFO @ Sun, 21 Jun 2020 22:40:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:40:24: #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 22:40:24: #1 tags after filtering in treatment: 18897552 INFO @ Sun, 21 Jun 2020 22:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:40:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:40:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:40:26: #2 number of paired peaks: 921 WARNING @ Sun, 21 Jun 2020 22:40:26: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Sun, 21 Jun 2020 22:40:26: start model_add_line... INFO @ Sun, 21 Jun 2020 22:40:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:40:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:40:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:40:26: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:40:26: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Sun, 21 Jun 2020 22:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05_model.r WARNING @ Sun, 21 Jun 2020 22:40:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:40:26: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Sun, 21 Jun 2020 22:40:26: #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 22:40:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:40:27: 14000000 INFO @ Sun, 21 Jun 2020 22:40:28: 9000000 INFO @ Sun, 21 Jun 2020 22:40:33: 15000000 INFO @ Sun, 21 Jun 2020 22:40:34: 10000000 INFO @ Sun, 21 Jun 2020 22:40:39: 16000000 INFO @ Sun, 21 Jun 2020 22:40:40: 11000000 INFO @ Sun, 21 Jun 2020 22:40:44: 17000000 INFO @ Sun, 21 Jun 2020 22:40:45: 12000000 INFO @ Sun, 21 Jun 2020 22:40:50: 18000000 INFO @ Sun, 21 Jun 2020 22:40:51: 13000000 INFO @ Sun, 21 Jun 2020 22:40:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:40:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:40:55: #1 total tags in treatment: 18897607 INFO @ Sun, 21 Jun 2020 22:40:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:40:55: #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 22:40:56: #1 tags after filtering in treatment: 18897552 INFO @ Sun, 21 Jun 2020 22:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:40:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:40:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:40:57: 14000000 INFO @ Sun, 21 Jun 2020 22:40:57: #2 number of paired peaks: 921 WARNING @ Sun, 21 Jun 2020 22:40:57: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Sun, 21 Jun 2020 22:40:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:40:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:40:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:40:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:40:58: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:40:58: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Sun, 21 Jun 2020 22:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10_model.r WARNING @ Sun, 21 Jun 2020 22:40:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:40:58: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Sun, 21 Jun 2020 22:40:58: #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 22:40:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:41:02: 15000000 INFO @ Sun, 21 Jun 2020 22:41:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:41:08: 16000000 INFO @ Sun, 21 Jun 2020 22:41:13: 17000000 INFO @ Sun, 21 Jun 2020 22:41:18: 18000000 INFO @ Sun, 21 Jun 2020 22:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.05_summits.bed INFO @ Sun, 21 Jun 2020 22:41:21: Done! pass1 - making usageList (666 chroms): 1 millis pass2 - checking and writing primary data (3530 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:41:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:41:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:41:23: #1 total tags in treatment: 18897607 INFO @ Sun, 21 Jun 2020 22:41:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:41:23: #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 22:41:24: #1 tags after filtering in treatment: 18897552 INFO @ Sun, 21 Jun 2020 22:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:41:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:41:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:41:25: #2 number of paired peaks: 921 WARNING @ Sun, 21 Jun 2020 22:41:25: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Sun, 21 Jun 2020 22:41:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:41:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:41:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:41:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:41:25: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 22:41:25: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Sun, 21 Jun 2020 22:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20_model.r WARNING @ Sun, 21 Jun 2020 22:41:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:41:25: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Sun, 21 Jun 2020 22:41:25: #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 22:41:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:41:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.10_summits.bed INFO @ Sun, 21 Jun 2020 22:41:53: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (2266 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:42:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:42:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827676/SRX6827676.20_summits.bed INFO @ Sun, 21 Jun 2020 22:42:20: Done! pass1 - making usageList (370 chroms): 1 millis pass2 - checking and writing primary data (973 records, 4 fields): 11 millis CompletedMACS2peakCalling