Job ID = 6459080 SRX = SRX6386757 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:59:49 prefetch.2.10.7: 1) Downloading 'SRR9624489'... 2020-06-21T12:59:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:06:09 prefetch.2.10.7: 1) 'SRR9624489' was downloaded successfully Read 43180409 spots for SRR9624489/SRR9624489.sra Written 43180409 spots for SRR9624489/SRR9624489.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: 00:08:54 43180409 reads; of these: 43180409 (100.00%) were unpaired; of these: 16900502 (39.14%) aligned 0 times 18828623 (43.60%) aligned exactly 1 time 7451284 (17.26%) aligned >1 times 60.86% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 18724366 / 26279907 = 0.7125 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 22:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.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 22:21:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:21:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:21:52: 1000000 INFO @ Sun, 21 Jun 2020 22:21:58: 2000000 INFO @ Sun, 21 Jun 2020 22:22:03: 3000000 INFO @ Sun, 21 Jun 2020 22:22:08: 4000000 INFO @ Sun, 21 Jun 2020 22:22:14: 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 22:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.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 22:22:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:22:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:20: 6000000 INFO @ Sun, 21 Jun 2020 22:22:23: 1000000 INFO @ Sun, 21 Jun 2020 22:22:25: 7000000 INFO @ Sun, 21 Jun 2020 22:22:29: 2000000 INFO @ Sun, 21 Jun 2020 22:22:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:22:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:22:29: #1 total tags in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:22:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:29: #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 22:22:29: #1 tags after filtering in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:30: #2 number of paired peaks: 2097 INFO @ Sun, 21 Jun 2020 22:22:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:30: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:22:30: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 22:22:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05_model.r WARNING @ Sun, 21 Jun 2020 22:22:30: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:30: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 22:22:30: #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 22:22:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:34: 3000000 INFO @ Sun, 21 Jun 2020 22:22:40: 4000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 22:22:45: 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 22:22:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.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 22:22:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:22:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:22:51: 6000000 INFO @ Sun, 21 Jun 2020 22:22:53: 1000000 INFO @ Sun, 21 Jun 2020 22:22:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:22:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:22:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.05_summits.bed INFO @ Sun, 21 Jun 2020 22:22:54: Done! pass1 - making usageList (932 chroms): 2 millis pass2 - checking and writing primary data (3817 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:22:57: 7000000 INFO @ Sun, 21 Jun 2020 22:22:59: 2000000 INFO @ Sun, 21 Jun 2020 22:23:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:00: #1 total tags in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:23:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:00: #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 22:23:01: #1 tags after filtering in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:01: #2 number of paired peaks: 2097 INFO @ Sun, 21 Jun 2020 22:23:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:02: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:23:02: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 22:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10_model.r WARNING @ Sun, 21 Jun 2020 22:23:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:02: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 22:23:02: #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 22:23:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:05: 3000000 INFO @ Sun, 21 Jun 2020 22:23:10: 4000000 INFO @ Sun, 21 Jun 2020 22:23:16: 5000000 INFO @ Sun, 21 Jun 2020 22:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.10_summits.bed INFO @ Sun, 21 Jun 2020 22:23:25: Done! pass1 - making usageList (700 chroms): 1 millis pass2 - checking and writing primary data (2634 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:28: 7000000 INFO @ Sun, 21 Jun 2020 22:23:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:23:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:23:31: #1 total tags in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:23:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:31: #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 22:23:31: #1 tags after filtering in treatment: 7555541 INFO @ Sun, 21 Jun 2020 22:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:32: #2 number of paired peaks: 2097 INFO @ Sun, 21 Jun 2020 22:23:32: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:32: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:32: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:32: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:32: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:23:32: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 22:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20_model.r WARNING @ Sun, 21 Jun 2020 22:23:32: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:32: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 22:23:32: #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 22:23:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:23:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386757/SRX6386757.20_summits.bed INFO @ Sun, 21 Jun 2020 22:23:56: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 15 millis CompletedMACS2peakCalling