Job ID = 6627076 SRX = SRX8347285 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:46:18 prefetch.2.10.7: 1) Downloading 'SRR11795468'... 2020-07-14T00:46:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:56:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:56:31 prefetch.2.10.7: 1) 'SRR11795468' was downloaded successfully 2020-07-14T00:56:31 prefetch.2.10.7: 'SRR11795468' has 0 unresolved dependencies Read 18429001 spots for SRR11795468/SRR11795468.sra Written 18429001 spots for SRR11795468/SRR11795468.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627418 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:10 18429001 reads; of these: 18429001 (100.00%) were paired; of these: 9763102 (52.98%) aligned concordantly 0 times 6468941 (35.10%) aligned concordantly exactly 1 time 2196958 (11.92%) aligned concordantly >1 times ---- 9763102 pairs aligned concordantly 0 times; of these: 710915 (7.28%) aligned discordantly 1 time ---- 9052187 pairs aligned 0 times concordantly or discordantly; of these: 18104374 mates make up the pairs; of these: 17309754 (95.61%) aligned 0 times 285010 (1.57%) aligned exactly 1 time 509610 (2.81%) aligned >1 times 53.04% overall alignment rate Time searching: 00:39:10 Overall time: 00:39:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 6055753 / 9340104 = 0.6484 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 @ Tue, 14 Jul 2020 10:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.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 @ Tue, 14 Jul 2020 10:44:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:44:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:44:19: 1000000 INFO @ Tue, 14 Jul 2020 10:44:30: 2000000 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 @ Tue, 14 Jul 2020 10:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.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 @ Tue, 14 Jul 2020 10:44:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:44:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:44:40: 3000000 INFO @ Tue, 14 Jul 2020 10:44:49: 1000000 INFO @ Tue, 14 Jul 2020 10:44:52: 4000000 INFO @ Tue, 14 Jul 2020 10:44:59: 2000000 INFO @ Tue, 14 Jul 2020 10:45:03: 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 @ Tue, 14 Jul 2020 10:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.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 @ Tue, 14 Jul 2020 10:45:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:45:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:45:09: 3000000 INFO @ Tue, 14 Jul 2020 10:45:14: 6000000 INFO @ Tue, 14 Jul 2020 10:45:19: 1000000 INFO @ Tue, 14 Jul 2020 10:45:19: 4000000 INFO @ Tue, 14 Jul 2020 10:45:26: 7000000 INFO @ Tue, 14 Jul 2020 10:45:30: 2000000 INFO @ Tue, 14 Jul 2020 10:45:31: 5000000 INFO @ Tue, 14 Jul 2020 10:45:31: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:45:31: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:45:31: #1 total tags in treatment: 2939881 INFO @ Tue, 14 Jul 2020 10:45:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:45:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:45:31: #1 tags after filtering in treatment: 2828587 INFO @ Tue, 14 Jul 2020 10:45:31: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:45:31: #1 finished! INFO @ Tue, 14 Jul 2020 10:45:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:45:31: #2 number of paired peaks: 1877 INFO @ Tue, 14 Jul 2020 10:45:31: start model_add_line... INFO @ Tue, 14 Jul 2020 10:45:31: start X-correlation... INFO @ Tue, 14 Jul 2020 10:45:31: end of X-cor INFO @ Tue, 14 Jul 2020 10:45:31: #2 finished! INFO @ Tue, 14 Jul 2020 10:45:31: #2 predicted fragment length is 247 bps INFO @ Tue, 14 Jul 2020 10:45:31: #2 alternative fragment length(s) may be 247 bps INFO @ Tue, 14 Jul 2020 10:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05_model.r WARNING @ Tue, 14 Jul 2020 10:45:31: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:45:31: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Tue, 14 Jul 2020 10:45:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:45:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:45:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:45:40: 3000000 INFO @ Tue, 14 Jul 2020 10:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.05_summits.bed INFO @ Tue, 14 Jul 2020 10:45:41: Done! INFO @ Tue, 14 Jul 2020 10:45:41: 6000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3510 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:45:49: 4000000 INFO @ Tue, 14 Jul 2020 10:45:51: 7000000 INFO @ Tue, 14 Jul 2020 10:45:55: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:45:55: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:45:55: #1 total tags in treatment: 2939881 INFO @ Tue, 14 Jul 2020 10:45:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:45:56: #1 tags after filtering in treatment: 2828587 INFO @ Tue, 14 Jul 2020 10:45:56: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:45:56: #1 finished! INFO @ Tue, 14 Jul 2020 10:45:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:45:56: #2 number of paired peaks: 1877 INFO @ Tue, 14 Jul 2020 10:45:56: start model_add_line... INFO @ Tue, 14 Jul 2020 10:45:56: start X-correlation... INFO @ Tue, 14 Jul 2020 10:45:56: end of X-cor INFO @ Tue, 14 Jul 2020 10:45:56: #2 finished! INFO @ Tue, 14 Jul 2020 10:45:56: #2 predicted fragment length is 247 bps INFO @ Tue, 14 Jul 2020 10:45:56: #2 alternative fragment length(s) may be 247 bps INFO @ Tue, 14 Jul 2020 10:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10_model.r WARNING @ Tue, 14 Jul 2020 10:45:56: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:45:56: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Tue, 14 Jul 2020 10:45:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:45:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:45:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:46:00: 5000000 INFO @ Tue, 14 Jul 2020 10:46:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:46:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.10_summits.bed INFO @ Tue, 14 Jul 2020 10:46:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2014 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:46:09: 6000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:46:18: 7000000 INFO @ Tue, 14 Jul 2020 10:46:22: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:46:22: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:46:22: #1 total tags in treatment: 2939881 INFO @ Tue, 14 Jul 2020 10:46:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:46:22: #1 tags after filtering in treatment: 2828587 INFO @ Tue, 14 Jul 2020 10:46:22: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:46:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:22: #2 number of paired peaks: 1877 INFO @ Tue, 14 Jul 2020 10:46:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:22: #2 predicted fragment length is 247 bps INFO @ Tue, 14 Jul 2020 10:46:22: #2 alternative fragment length(s) may be 247 bps INFO @ Tue, 14 Jul 2020 10:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20_model.r WARNING @ Tue, 14 Jul 2020 10:46:22: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:22: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Tue, 14 Jul 2020 10:46:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:46:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:46:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347285/SRX8347285.20_summits.bed INFO @ Tue, 14 Jul 2020 10:46:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (819 records, 4 fields): 2 millis CompletedMACS2peakCalling