Job ID = 6457546 SRX = SRX4669035 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:56:33 prefetch.2.10.7: 1) Downloading 'SRR7817560'... 2020-06-21T11:56:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:57:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:57:08 prefetch.2.10.7: 'SRR7817560' is valid 2020-06-21T11:57:08 prefetch.2.10.7: 1) 'SRR7817560' was downloaded successfully 2020-06-21T11:57:08 prefetch.2.10.7: 'SRR7817560' has 0 unresolved dependencies Read 10612405 spots for SRR7817560/SRR7817560.sra Written 10612405 spots for SRR7817560/SRR7817560.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: 00:03:17 10612405 reads; of these: 10612405 (100.00%) were unpaired; of these: 473649 (4.46%) aligned 0 times 6204794 (58.47%) aligned exactly 1 time 3933962 (37.07%) aligned >1 times 95.54% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 2600200 / 10138756 = 0.2565 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 21:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.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 21:03:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:28: 1000000 INFO @ Sun, 21 Jun 2020 21:03:33: 2000000 INFO @ Sun, 21 Jun 2020 21:03:39: 3000000 INFO @ Sun, 21 Jun 2020 21:03:45: 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 21:03:50: 5000000 INFO @ Sun, 21 Jun 2020 21:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.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 21:03:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:57: 6000000 INFO @ Sun, 21 Jun 2020 21:03:59: 1000000 INFO @ Sun, 21 Jun 2020 21:04:04: 7000000 INFO @ Sun, 21 Jun 2020 21:04:06: 2000000 INFO @ Sun, 21 Jun 2020 21:04:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:04:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:04:08: #1 total tags in treatment: 7538556 INFO @ Sun, 21 Jun 2020 21:04:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:08: #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 21:04:08: #1 tags after filtering in treatment: 7538523 INFO @ Sun, 21 Jun 2020 21:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:08: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:09: #2 number of paired peaks: 1949 INFO @ Sun, 21 Jun 2020 21:04:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:09: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:04:09: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05_model.r WARNING @ Sun, 21 Jun 2020 21:04:09: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:04:09: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:04:09: #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 21:04:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:13: 3000000 INFO @ Sun, 21 Jun 2020 21:04:20: 4000000 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 21:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.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 21:04:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:27: 5000000 INFO @ Sun, 21 Jun 2020 21:04:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:04:29: 1000000 INFO @ Sun, 21 Jun 2020 21:04:34: 6000000 INFO @ Sun, 21 Jun 2020 21:04:35: 2000000 INFO @ Sun, 21 Jun 2020 21:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.05_summits.bed INFO @ Sun, 21 Jun 2020 21:04:37: Done! pass1 - making usageList (467 chroms): 2 millis pass2 - checking and writing primary data (4276 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:04:42: 7000000 INFO @ Sun, 21 Jun 2020 21:04:42: 3000000 INFO @ Sun, 21 Jun 2020 21:04:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:04:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:04:46: #1 total tags in treatment: 7538556 INFO @ Sun, 21 Jun 2020 21:04:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:04:46: #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 21:04:46: #1 tags after filtering in treatment: 7538523 INFO @ Sun, 21 Jun 2020 21:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:04:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:04:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:04:47: #2 number of paired peaks: 1949 INFO @ Sun, 21 Jun 2020 21:04:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:04:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:04:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:04:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:04:47: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:04:47: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10_model.r WARNING @ Sun, 21 Jun 2020 21:04:47: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:04:47: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:04:47: #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 21:04:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:04:48: 4000000 INFO @ Sun, 21 Jun 2020 21:04:54: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:05:00: 6000000 INFO @ Sun, 21 Jun 2020 21:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:06: 7000000 INFO @ Sun, 21 Jun 2020 21:05:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:05:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:05:09: #1 total tags in treatment: 7538556 INFO @ Sun, 21 Jun 2020 21:05:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:09: #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 21:05:10: #1 tags after filtering in treatment: 7538523 INFO @ Sun, 21 Jun 2020 21:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:10: #2 number of paired peaks: 1949 INFO @ Sun, 21 Jun 2020 21:05:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:10: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 21:05:10: #2 alternative fragment length(s) may be 4,100 bps INFO @ Sun, 21 Jun 2020 21:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20_model.r WARNING @ Sun, 21 Jun 2020 21:05:10: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:05:10: #2 You may need to consider one of the other alternative d(s): 4,100 WARNING @ Sun, 21 Jun 2020 21:05:10: #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 21:05:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.10_summits.bed INFO @ Sun, 21 Jun 2020 21:05:14: Done! pass1 - making usageList (296 chroms): 1 millis pass2 - checking and writing primary data (1454 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:05:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669035/SRX4669035.20_summits.bed INFO @ Sun, 21 Jun 2020 21:05:37: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 11 millis CompletedMACS2peakCalling