Job ID = 6454415 SRX = SRX2055947 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:12:39 prefetch.2.10.7: 1) Downloading 'SRR4069179'... 2020-06-21T09:12:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:37 prefetch.2.10.7: 1) 'SRR4069179' was downloaded successfully Read 22695222 spots for SRR4069179/SRR4069179.sra Written 22695222 spots for SRR4069179/SRR4069179.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: 00:07:16 22695222 reads; of these: 22695222 (100.00%) were unpaired; of these: 3080514 (13.57%) aligned 0 times 12142340 (53.50%) aligned exactly 1 time 7472368 (32.92%) aligned >1 times 86.43% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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] 4585200 / 19614708 = 0.2338 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 18:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.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 18:33:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:42: 1000000 INFO @ Sun, 21 Jun 2020 18:33:48: 2000000 INFO @ Sun, 21 Jun 2020 18:33:54: 3000000 INFO @ Sun, 21 Jun 2020 18:34:00: 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 18:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.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 18:34:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:06: 5000000 INFO @ Sun, 21 Jun 2020 18:34:12: 1000000 INFO @ Sun, 21 Jun 2020 18:34:12: 6000000 INFO @ Sun, 21 Jun 2020 18:34:18: 2000000 INFO @ Sun, 21 Jun 2020 18:34:18: 7000000 INFO @ Sun, 21 Jun 2020 18:34:24: 3000000 INFO @ Sun, 21 Jun 2020 18:34:24: 8000000 INFO @ Sun, 21 Jun 2020 18:34:30: 4000000 INFO @ Sun, 21 Jun 2020 18:34:30: 9000000 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 18:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.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 18:34:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:37: 5000000 INFO @ Sun, 21 Jun 2020 18:34:37: 10000000 INFO @ Sun, 21 Jun 2020 18:34:42: 1000000 INFO @ Sun, 21 Jun 2020 18:34:43: 6000000 INFO @ Sun, 21 Jun 2020 18:34:43: 11000000 INFO @ Sun, 21 Jun 2020 18:34:49: 2000000 INFO @ Sun, 21 Jun 2020 18:34:49: 7000000 INFO @ Sun, 21 Jun 2020 18:34:49: 12000000 INFO @ Sun, 21 Jun 2020 18:34:55: 8000000 INFO @ Sun, 21 Jun 2020 18:34:55: 3000000 INFO @ Sun, 21 Jun 2020 18:34:56: 13000000 INFO @ Sun, 21 Jun 2020 18:35:01: 9000000 INFO @ Sun, 21 Jun 2020 18:35:02: 4000000 INFO @ Sun, 21 Jun 2020 18:35:02: 14000000 INFO @ Sun, 21 Jun 2020 18:35:07: 10000000 INFO @ Sun, 21 Jun 2020 18:35:08: 5000000 INFO @ Sun, 21 Jun 2020 18:35:09: 15000000 INFO @ Sun, 21 Jun 2020 18:35:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:35:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:35:09: #1 total tags in treatment: 15029508 INFO @ Sun, 21 Jun 2020 18:35:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:09: #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 18:35:10: #1 tags after filtering in treatment: 15029437 INFO @ Sun, 21 Jun 2020 18:35:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:11: #2 number of paired peaks: 2313 INFO @ Sun, 21 Jun 2020 18:35:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:11: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:35:11: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 18:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05_model.r WARNING @ Sun, 21 Jun 2020 18:35:11: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:11: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 18:35:11: #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 18:35:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:13: 11000000 INFO @ Sun, 21 Jun 2020 18:35:14: 6000000 INFO @ Sun, 21 Jun 2020 18:35:20: 12000000 INFO @ Sun, 21 Jun 2020 18:35:21: 7000000 INFO @ Sun, 21 Jun 2020 18:35:26: 13000000 INFO @ Sun, 21 Jun 2020 18:35:27: 8000000 INFO @ Sun, 21 Jun 2020 18:35:33: 14000000 INFO @ Sun, 21 Jun 2020 18:35:33: 9000000 INFO @ Sun, 21 Jun 2020 18:35:39: 15000000 INFO @ Sun, 21 Jun 2020 18:35:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:35:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:35:39: #1 total tags in treatment: 15029508 INFO @ Sun, 21 Jun 2020 18:35:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:39: #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 18:35:39: 10000000 INFO @ Sun, 21 Jun 2020 18:35:40: #1 tags after filtering in treatment: 15029437 INFO @ Sun, 21 Jun 2020 18:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:41: #2 number of paired peaks: 2313 INFO @ Sun, 21 Jun 2020 18:35:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:41: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:35:41: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 18:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:41: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:41: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 18:35:41: #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 18:35:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:46: 11000000 INFO @ Sun, 21 Jun 2020 18:35:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:35:52: 12000000 INFO @ Sun, 21 Jun 2020 18:35:58: 13000000 INFO @ Sun, 21 Jun 2020 18:36:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:03: Done! pass1 - making usageList (694 chroms): 1 millis pass2 - checking and writing primary data (3868 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:05: 14000000 INFO @ Sun, 21 Jun 2020 18:36:11: 15000000 INFO @ Sun, 21 Jun 2020 18:36:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:36:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:36:11: #1 total tags in treatment: 15029508 INFO @ Sun, 21 Jun 2020 18:36:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:11: #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 18:36:12: #1 tags after filtering in treatment: 15029437 INFO @ Sun, 21 Jun 2020 18:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:13: #2 number of paired peaks: 2313 INFO @ Sun, 21 Jun 2020 18:36:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:13: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:36:13: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 18:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20_model.r WARNING @ Sun, 21 Jun 2020 18:36:13: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:36:13: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 18:36:13: #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 18:36:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.10_summits.bed INFO @ Sun, 21 Jun 2020 18:36:32: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2397 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055947/SRX2055947.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:05: Done! pass1 - making usageList (477 chroms): 2 millis pass2 - checking and writing primary data (1682 records, 4 fields): 17 millis CompletedMACS2peakCalling