Job ID = 6454434 SRX = SRX2055962 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:04:34 prefetch.2.10.7: 1) Downloading 'SRR4069194'... 2020-06-21T09:04:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:21 prefetch.2.10.7: 'SRR4069194' is valid 2020-06-21T09:06:21 prefetch.2.10.7: 1) 'SRR4069194' was downloaded successfully Read 20909517 spots for SRR4069194/SRR4069194.sra Written 20909517 spots for SRR4069194/SRR4069194.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: 00:07:22 20909517 reads; of these: 20909517 (100.00%) were unpaired; of these: 932212 (4.46%) aligned 0 times 13045712 (62.39%) aligned exactly 1 time 6931593 (33.15%) aligned >1 times 95.54% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 3181785 / 19977305 = 0.1593 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 18:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.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 18:18:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:01: 1000000 INFO @ Sun, 21 Jun 2020 18:19:07: 2000000 INFO @ Sun, 21 Jun 2020 18:19:13: 3000000 INFO @ Sun, 21 Jun 2020 18:19:19: 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 18:19:25: 5000000 INFO @ Sun, 21 Jun 2020 18:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.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 18:19:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:31: 1000000 INFO @ Sun, 21 Jun 2020 18:19:32: 6000000 INFO @ Sun, 21 Jun 2020 18:19:37: 2000000 INFO @ Sun, 21 Jun 2020 18:19:38: 7000000 INFO @ Sun, 21 Jun 2020 18:19:42: 3000000 INFO @ Sun, 21 Jun 2020 18:19:44: 8000000 INFO @ Sun, 21 Jun 2020 18:19:47: 4000000 INFO @ Sun, 21 Jun 2020 18:19:51: 9000000 INFO @ Sun, 21 Jun 2020 18:19:52: 5000000 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 18:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.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 18:19:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:57: 10000000 INFO @ Sun, 21 Jun 2020 18:19:58: 6000000 INFO @ Sun, 21 Jun 2020 18:20:02: 1000000 INFO @ Sun, 21 Jun 2020 18:20:03: 11000000 INFO @ Sun, 21 Jun 2020 18:20:03: 7000000 INFO @ Sun, 21 Jun 2020 18:20:09: 8000000 INFO @ Sun, 21 Jun 2020 18:20:09: 2000000 INFO @ Sun, 21 Jun 2020 18:20:09: 12000000 INFO @ Sun, 21 Jun 2020 18:20:14: 9000000 INFO @ Sun, 21 Jun 2020 18:20:15: 13000000 INFO @ Sun, 21 Jun 2020 18:20:16: 3000000 INFO @ Sun, 21 Jun 2020 18:20:19: 10000000 INFO @ Sun, 21 Jun 2020 18:20:22: 14000000 INFO @ Sun, 21 Jun 2020 18:20:22: 4000000 INFO @ Sun, 21 Jun 2020 18:20:24: 11000000 INFO @ Sun, 21 Jun 2020 18:20:29: 15000000 INFO @ Sun, 21 Jun 2020 18:20:29: 5000000 INFO @ Sun, 21 Jun 2020 18:20:30: 12000000 INFO @ Sun, 21 Jun 2020 18:20:35: 13000000 INFO @ Sun, 21 Jun 2020 18:20:35: 16000000 INFO @ Sun, 21 Jun 2020 18:20:36: 6000000 INFO @ Sun, 21 Jun 2020 18:20:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:41: #1 total tags in treatment: 16795520 INFO @ Sun, 21 Jun 2020 18:20:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:41: #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 18:20:41: 14000000 INFO @ Sun, 21 Jun 2020 18:20:41: #1 tags after filtering in treatment: 16795451 INFO @ Sun, 21 Jun 2020 18:20:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:43: #2 number of paired peaks: 1765 INFO @ Sun, 21 Jun 2020 18:20:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:43: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:20:43: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:43: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:43: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:20:43: #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 18:20:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:43: 7000000 INFO @ Sun, 21 Jun 2020 18:20:46: 15000000 INFO @ Sun, 21 Jun 2020 18:20:50: 8000000 INFO @ Sun, 21 Jun 2020 18:20:51: 16000000 INFO @ Sun, 21 Jun 2020 18:20:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:56: #1 total tags in treatment: 16795520 INFO @ Sun, 21 Jun 2020 18:20:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:56: #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 18:20:56: #1 tags after filtering in treatment: 16795451 INFO @ Sun, 21 Jun 2020 18:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:57: 9000000 INFO @ Sun, 21 Jun 2020 18:20:58: #2 number of paired peaks: 1765 INFO @ Sun, 21 Jun 2020 18:20:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:58: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:20:58: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:58: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:20:58: #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 18:20:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:03: 10000000 INFO @ Sun, 21 Jun 2020 18:21:09: 11000000 INFO @ Sun, 21 Jun 2020 18:21:15: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:21: 13000000 INFO @ Sun, 21 Jun 2020 18:21:27: 14000000 INFO @ Sun, 21 Jun 2020 18:21:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:33: 15000000 INFO @ Sun, 21 Jun 2020 18:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:37: Done! pass1 - making usageList (678 chroms): 1 millis pass2 - checking and writing primary data (3175 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:39: 16000000 INFO @ Sun, 21 Jun 2020 18:21:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:44: #1 total tags in treatment: 16795520 INFO @ Sun, 21 Jun 2020 18:21:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:44: #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 18:21:45: #1 tags after filtering in treatment: 16795451 INFO @ Sun, 21 Jun 2020 18:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:46: #2 number of paired peaks: 1765 INFO @ Sun, 21 Jun 2020 18:21:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:46: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:21:46: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 18:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:46: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 18:21:46: #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 18:21:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:50: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (2173 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055962/SRX2055962.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:38: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (1471 records, 4 fields): 14 millis CompletedMACS2peakCalling