Job ID = 6457039 SRX = SRX4370068 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:19:54 prefetch.2.10.7: 1) Downloading 'SRR7500645'... 2020-06-21T11:19:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:10 prefetch.2.10.7: 'SRR7500645' is valid 2020-06-21T11:21:10 prefetch.2.10.7: 1) 'SRR7500645' was downloaded successfully 2020-06-21T11:21:10 prefetch.2.10.7: 'SRR7500645' has 0 unresolved dependencies Read 13198671 spots for SRR7500645/SRR7500645.sra Written 13198671 spots for SRR7500645/SRR7500645.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: 00:03:25 13198671 reads; of these: 13198671 (100.00%) were unpaired; of these: 684450 (5.19%) aligned 0 times 8957613 (67.87%) aligned exactly 1 time 3556608 (26.95%) aligned >1 times 94.81% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 3973432 / 12514221 = 0.3175 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 20:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.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 20:27:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:00: 1000000 INFO @ Sun, 21 Jun 2020 20:28:05: 2000000 INFO @ Sun, 21 Jun 2020 20:28:11: 3000000 INFO @ Sun, 21 Jun 2020 20:28:16: 4000000 INFO @ Sun, 21 Jun 2020 20:28:21: 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 20:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.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 20:28:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:26: 6000000 INFO @ Sun, 21 Jun 2020 20:28:31: 1000000 INFO @ Sun, 21 Jun 2020 20:28:31: 7000000 INFO @ Sun, 21 Jun 2020 20:28:36: 2000000 INFO @ Sun, 21 Jun 2020 20:28:37: 8000000 INFO @ Sun, 21 Jun 2020 20:28:40: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:28:40: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:28:40: #1 total tags in treatment: 8540789 INFO @ Sun, 21 Jun 2020 20:28:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:40: #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 20:28:40: #1 tags after filtering in treatment: 8540681 INFO @ Sun, 21 Jun 2020 20:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:41: #2 number of paired peaks: 2475 INFO @ Sun, 21 Jun 2020 20:28:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:41: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:28:41: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 20:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05_model.r WARNING @ Sun, 21 Jun 2020 20:28:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:41: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 20:28:41: #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 20:28:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:42: 3000000 INFO @ Sun, 21 Jun 2020 20:28:48: 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 20:28:53: 5000000 INFO @ Sun, 21 Jun 2020 20:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.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 20:28:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:59: 6000000 INFO @ Sun, 21 Jun 2020 20:28:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:00: 1000000 INFO @ Sun, 21 Jun 2020 20:29:04: 7000000 INFO @ Sun, 21 Jun 2020 20:29:05: 2000000 INFO @ Sun, 21 Jun 2020 20:29:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.05_summits.bed INFO @ Sun, 21 Jun 2020 20:29:08: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (2081 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:29:10: 3000000 INFO @ Sun, 21 Jun 2020 20:29:10: 8000000 INFO @ Sun, 21 Jun 2020 20:29:14: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:29:14: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:29:14: #1 total tags in treatment: 8540789 INFO @ Sun, 21 Jun 2020 20:29:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:14: #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 20:29:14: #1 tags after filtering in treatment: 8540681 INFO @ Sun, 21 Jun 2020 20:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:15: #2 number of paired peaks: 2475 INFO @ Sun, 21 Jun 2020 20:29:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:15: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:29:15: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 20:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10_model.r WARNING @ Sun, 21 Jun 2020 20:29:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:15: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 20:29:15: #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 20:29:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:15: 4000000 INFO @ Sun, 21 Jun 2020 20:29:20: 5000000 INFO @ Sun, 21 Jun 2020 20:29:25: 6000000 INFO @ Sun, 21 Jun 2020 20:29:30: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:35: 8000000 INFO @ Sun, 21 Jun 2020 20:29:38: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:29:38: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:29:38: #1 total tags in treatment: 8540789 INFO @ Sun, 21 Jun 2020 20:29:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:38: #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 20:29:38: #1 tags after filtering in treatment: 8540681 INFO @ Sun, 21 Jun 2020 20:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:39: #2 number of paired peaks: 2475 INFO @ Sun, 21 Jun 2020 20:29:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:39: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:29:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 20:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20_model.r WARNING @ Sun, 21 Jun 2020 20:29:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 20:29:39: #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 20:29:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.10_summits.bed INFO @ Sun, 21 Jun 2020 20:29:42: Done! pass1 - making usageList (242 chroms): 1 millis pass2 - checking and writing primary data (833 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:29:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370068/SRX4370068.20_summits.bed INFO @ Sun, 21 Jun 2020 20:30:06: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 6 millis CompletedMACS2peakCalling