Job ID = 6456616 SRX = SRX372809 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:24 prefetch.2.10.7: 1) Downloading 'SRR1023765'... 2020-06-21T11:21:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:27:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:27:05 prefetch.2.10.7: 1) 'SRR1023765' was downloaded successfully Read 21201163 spots for SRR1023765/SRR1023765.sra Written 21201163 spots for SRR1023765/SRR1023765.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: 00:06:04 21201163 reads; of these: 21201163 (100.00%) were unpaired; of these: 1230929 (5.81%) aligned 0 times 13714037 (64.69%) aligned exactly 1 time 6256197 (29.51%) aligned >1 times 94.19% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 8320811 / 19970234 = 0.4167 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 20:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.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 20:38:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:56: 1000000 INFO @ Sun, 21 Jun 2020 20:39:02: 2000000 INFO @ Sun, 21 Jun 2020 20:39:07: 3000000 INFO @ Sun, 21 Jun 2020 20:39:13: 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 20:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.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 20:39:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:19: 5000000 INFO @ Sun, 21 Jun 2020 20:39:25: 1000000 INFO @ Sun, 21 Jun 2020 20:39:25: 6000000 INFO @ Sun, 21 Jun 2020 20:39:32: 2000000 INFO @ Sun, 21 Jun 2020 20:39:32: 7000000 INFO @ Sun, 21 Jun 2020 20:39:38: 3000000 INFO @ Sun, 21 Jun 2020 20:39:38: 8000000 INFO @ Sun, 21 Jun 2020 20:39:44: 4000000 INFO @ Sun, 21 Jun 2020 20:39:45: 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 20:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.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 20:39:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:51: 5000000 INFO @ Sun, 21 Jun 2020 20:39:52: 10000000 INFO @ Sun, 21 Jun 2020 20:39:57: 1000000 INFO @ Sun, 21 Jun 2020 20:39:58: 6000000 INFO @ Sun, 21 Jun 2020 20:39:59: 11000000 INFO @ Sun, 21 Jun 2020 20:40:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:04: #1 total tags in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:40:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:04: #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 20:40:05: #1 tags after filtering in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:06: #2 number of paired peaks: 1229 INFO @ Sun, 21 Jun 2020 20:40:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:06: 7000000 INFO @ Sun, 21 Jun 2020 20:40:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:06: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:40:06: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 20:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05_model.r WARNING @ Sun, 21 Jun 2020 20:40:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:06: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 20:40:06: #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 20:40:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:06: 2000000 INFO @ Sun, 21 Jun 2020 20:40:13: 8000000 INFO @ Sun, 21 Jun 2020 20:40:14: 3000000 INFO @ Sun, 21 Jun 2020 20:40:20: 9000000 INFO @ Sun, 21 Jun 2020 20:40:23: 4000000 INFO @ Sun, 21 Jun 2020 20:40:28: 10000000 INFO @ Sun, 21 Jun 2020 20:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:31: 5000000 INFO @ Sun, 21 Jun 2020 20:40:35: 11000000 INFO @ Sun, 21 Jun 2020 20:40:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.05_summits.bed INFO @ Sun, 21 Jun 2020 20:40:40: Done! INFO @ Sun, 21 Jun 2020 20:40:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:40: #1 total tags in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:40:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (757 chroms): 1 millis pass2 - checking and writing primary data (3529 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:41: #1 tags after filtering in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:42: #2 number of paired peaks: 1229 INFO @ Sun, 21 Jun 2020 20:40:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:42: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:40:42: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 20:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10_model.r WARNING @ Sun, 21 Jun 2020 20:40:42: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:42: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 20:40:42: #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 20:40:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:48: 7000000 INFO @ Sun, 21 Jun 2020 20:40:55: 8000000 INFO @ Sun, 21 Jun 2020 20:41:03: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:10: 10000000 INFO @ Sun, 21 Jun 2020 20:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:16: Done! pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (2542 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:17: 11000000 INFO @ Sun, 21 Jun 2020 20:41:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:22: #1 total tags in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:41:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:22: #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 20:41:22: #1 tags after filtering in treatment: 11649423 INFO @ Sun, 21 Jun 2020 20:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:23: #2 number of paired peaks: 1229 INFO @ Sun, 21 Jun 2020 20:41:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:23: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:41:23: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 20:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20_model.r WARNING @ Sun, 21 Jun 2020 20:41:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:23: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 20:41:23: #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 20:41:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX372809/SRX372809.20_summits.bed INFO @ Sun, 21 Jun 2020 20:41:58: Done! pass1 - making usageList (483 chroms): 2 millis pass2 - checking and writing primary data (1428 records, 4 fields): 16 millis CompletedMACS2peakCalling