Job ID = 6627079 SRX = SRX8347287 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:46:47 prefetch.2.10.7: 1) Downloading 'SRR11795470'... 2020-07-14T00:46:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:55:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:55:33 prefetch.2.10.7: 1) 'SRR11795470' was downloaded successfully 2020-07-14T00:55:33 prefetch.2.10.7: 'SRR11795470' has 0 unresolved dependencies Read 19203481 spots for SRR11795470/SRR11795470.sra Written 19203481 spots for SRR11795470/SRR11795470.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627422 ("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: 00:42:28 19203481 reads; of these: 19203481 (100.00%) were paired; of these: 9415745 (49.03%) aligned concordantly 0 times 7310184 (38.07%) aligned concordantly exactly 1 time 2477552 (12.90%) aligned concordantly >1 times ---- 9415745 pairs aligned concordantly 0 times; of these: 747100 (7.93%) aligned discordantly 1 time ---- 8668645 pairs aligned 0 times concordantly or discordantly; of these: 17337290 mates make up the pairs; of these: 16464497 (94.97%) aligned 0 times 315703 (1.82%) aligned exactly 1 time 557090 (3.21%) aligned >1 times 57.13% overall alignment rate Time searching: 00:42:28 Overall time: 00:42:28 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] 7027434 / 10495749 = 0.6696 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 10:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.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 10:47:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:23: 1000000 INFO @ Tue, 14 Jul 2020 10:47:33: 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 10:47:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.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 10:47:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:43: 3000000 INFO @ Tue, 14 Jul 2020 10:47:53: 1000000 INFO @ Tue, 14 Jul 2020 10:47:54: 4000000 INFO @ Tue, 14 Jul 2020 10:48:03: 2000000 INFO @ Tue, 14 Jul 2020 10:48:05: 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 10:48:13: 3000000 INFO @ Tue, 14 Jul 2020 10:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.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 10:48:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:48:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:48:15: 6000000 INFO @ Tue, 14 Jul 2020 10:48:23: 4000000 INFO @ Tue, 14 Jul 2020 10:48:24: 1000000 INFO @ Tue, 14 Jul 2020 10:48:26: 7000000 INFO @ Tue, 14 Jul 2020 10:48:33: 5000000 INFO @ Tue, 14 Jul 2020 10:48:34: 2000000 INFO @ Tue, 14 Jul 2020 10:48:35: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:48:35: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:48:35: #1 total tags in treatment: 3116158 INFO @ Tue, 14 Jul 2020 10:48:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:48:35: #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 10:48:35: #1 tags after filtering in treatment: 2986351 INFO @ Tue, 14 Jul 2020 10:48:35: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:48:35: #1 finished! INFO @ Tue, 14 Jul 2020 10:48:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:48:35: #2 number of paired peaks: 2067 INFO @ Tue, 14 Jul 2020 10:48:35: start model_add_line... INFO @ Tue, 14 Jul 2020 10:48:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:48:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:48:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:48:36: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 10:48:36: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 10:48:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05_model.r WARNING @ Tue, 14 Jul 2020 10:48:36: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:48:36: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Tue, 14 Jul 2020 10:48:36: #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 10:48:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:48:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:43: 6000000 INFO @ Tue, 14 Jul 2020 10:48:43: 3000000 INFO @ Tue, 14 Jul 2020 10:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.05_summits.bed INFO @ Tue, 14 Jul 2020 10:48:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3744 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:48:52: 7000000 INFO @ Tue, 14 Jul 2020 10:48:53: 4000000 INFO @ Tue, 14 Jul 2020 10:49:00: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:49:00: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:49:00: #1 total tags in treatment: 3116158 INFO @ Tue, 14 Jul 2020 10:49:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:00: #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 10:49:00: #1 tags after filtering in treatment: 2986351 INFO @ Tue, 14 Jul 2020 10:49:00: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:49:00: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:01: #2 number of paired peaks: 2067 INFO @ Tue, 14 Jul 2020 10:49:01: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:01: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:01: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:01: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:01: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 10:49:01: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 10:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10_model.r WARNING @ Tue, 14 Jul 2020 10:49:01: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:01: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Tue, 14 Jul 2020 10:49:01: #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 10:49:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:49:02: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:49:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:11: 6000000 INFO @ Tue, 14 Jul 2020 10:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.10_summits.bed INFO @ Tue, 14 Jul 2020 10:49:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2238 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:20: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:49:28: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:49:28: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:49:28: #1 total tags in treatment: 3116158 INFO @ Tue, 14 Jul 2020 10:49:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:28: #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 10:49:28: #1 tags after filtering in treatment: 2986351 INFO @ Tue, 14 Jul 2020 10:49:28: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:49:28: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:28: #2 number of paired peaks: 2067 INFO @ Tue, 14 Jul 2020 10:49:28: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:28: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:28: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:28: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:28: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 10:49:28: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 10:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20_model.r WARNING @ Tue, 14 Jul 2020 10:49:28: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:28: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Tue, 14 Jul 2020 10:49:28: #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 10:49:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:49:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347287/SRX8347287.20_summits.bed INFO @ Tue, 14 Jul 2020 10:49:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (996 records, 4 fields): 3 millis CompletedMACS2peakCalling