Job ID = 6457949 SRX = SRX4923193 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:04:07 prefetch.2.10.7: 1) Downloading 'SRR8096343'... 2020-06-21T12:04:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:06:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:06:38 prefetch.2.10.7: 1) 'SRR8096343' was downloaded successfully 2020-06-21T12:06:38 prefetch.2.10.7: 'SRR8096343' has 0 unresolved dependencies Read 32601466 spots for SRR8096343/SRR8096343.sra Written 32601466 spots for SRR8096343/SRR8096343.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: 00:14:00 32601466 reads; of these: 32601466 (100.00%) were unpaired; of these: 814925 (2.50%) aligned 0 times 6628893 (20.33%) aligned exactly 1 time 25157648 (77.17%) aligned >1 times 97.50% overall alignment rate Time searching: 00:14:00 Overall time: 00:14:00 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 16 files... [bam_rmdupse_core] 18462993 / 31786541 = 0.5808 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 21:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.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 21:27:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:10: 1000000 INFO @ Sun, 21 Jun 2020 21:27:15: 2000000 INFO @ Sun, 21 Jun 2020 21:27:20: 3000000 INFO @ Sun, 21 Jun 2020 21:27:25: 4000000 INFO @ Sun, 21 Jun 2020 21:27:30: 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 21:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.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 21:27:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:35: 6000000 INFO @ Sun, 21 Jun 2020 21:27:40: 1000000 INFO @ Sun, 21 Jun 2020 21:27:41: 7000000 INFO @ Sun, 21 Jun 2020 21:27:45: 2000000 INFO @ Sun, 21 Jun 2020 21:27:46: 8000000 INFO @ Sun, 21 Jun 2020 21:27:50: 3000000 INFO @ Sun, 21 Jun 2020 21:27:52: 9000000 INFO @ Sun, 21 Jun 2020 21:27:56: 4000000 INFO @ Sun, 21 Jun 2020 21:27:57: 10000000 INFO @ Sun, 21 Jun 2020 21:28:01: 5000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:28:02: 11000000 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 21:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.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 21:28:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:07: 6000000 INFO @ Sun, 21 Jun 2020 21:28:08: 12000000 INFO @ Sun, 21 Jun 2020 21:28:12: 1000000 INFO @ Sun, 21 Jun 2020 21:28:12: 7000000 INFO @ Sun, 21 Jun 2020 21:28:14: 13000000 INFO @ Sun, 21 Jun 2020 21:28:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:16: #1 total tags in treatment: 13323548 INFO @ Sun, 21 Jun 2020 21:28:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:16: #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 21:28:16: #1 tags after filtering in treatment: 13323488 INFO @ Sun, 21 Jun 2020 21:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:17: 2000000 INFO @ Sun, 21 Jun 2020 21:28:18: 8000000 INFO @ Sun, 21 Jun 2020 21:28:18: #2 number of paired peaks: 10469 INFO @ Sun, 21 Jun 2020 21:28:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:18: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:28:18: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 21 Jun 2020 21:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05_model.r WARNING @ Sun, 21 Jun 2020 21:28:18: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:18: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 21 Jun 2020 21:28:18: #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 21:28:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:23: 3000000 INFO @ Sun, 21 Jun 2020 21:28:24: 9000000 INFO @ Sun, 21 Jun 2020 21:28:29: 4000000 INFO @ Sun, 21 Jun 2020 21:28:30: 10000000 INFO @ Sun, 21 Jun 2020 21:28:34: 5000000 INFO @ Sun, 21 Jun 2020 21:28:35: 11000000 INFO @ Sun, 21 Jun 2020 21:28:40: 6000000 INFO @ Sun, 21 Jun 2020 21:28:41: 12000000 INFO @ Sun, 21 Jun 2020 21:28:45: 7000000 INFO @ Sun, 21 Jun 2020 21:28:47: 13000000 INFO @ Sun, 21 Jun 2020 21:28:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:49: #1 total tags in treatment: 13323548 INFO @ Sun, 21 Jun 2020 21:28:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:49: #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 21:28:49: #1 tags after filtering in treatment: 13323488 INFO @ Sun, 21 Jun 2020 21:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:51: 8000000 INFO @ Sun, 21 Jun 2020 21:28:51: #2 number of paired peaks: 10469 INFO @ Sun, 21 Jun 2020 21:28:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:51: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 21 Jun 2020 21:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10_model.r WARNING @ Sun, 21 Jun 2020 21:28:51: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:51: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 21 Jun 2020 21:28:51: #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 21:28:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:28:57: 9000000 INFO @ Sun, 21 Jun 2020 21:29:03: 10000000 INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:03: Done! pass1 - making usageList (1227 chroms): 3 millis pass2 - checking and writing primary data (9894 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:08: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:29:14: 12000000 INFO @ Sun, 21 Jun 2020 21:29:20: 13000000 INFO @ Sun, 21 Jun 2020 21:29:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:22: #1 total tags in treatment: 13323548 INFO @ Sun, 21 Jun 2020 21:29:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:22: #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 21:29:22: #1 tags after filtering in treatment: 13323488 INFO @ Sun, 21 Jun 2020 21:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:24: #2 number of paired peaks: 10469 INFO @ Sun, 21 Jun 2020 21:29:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:24: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:29:24: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 21 Jun 2020 21:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20_model.r WARNING @ Sun, 21 Jun 2020 21:29:24: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:24: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 21 Jun 2020 21:29:24: #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 21:29:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:34: Done! pass1 - making usageList (1102 chroms): 1 millis pass2 - checking and writing primary data (5152 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923193/SRX4923193.20_summits.bed INFO @ Sun, 21 Jun 2020 21:30:07: Done! pass1 - making usageList (915 chroms): 1 millis pass2 - checking and writing primary data (2901 records, 4 fields): 28 millis CompletedMACS2peakCalling