Job ID = 5721087 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,348,191 reads read : 16,696,382 reads written : 16,696,382 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 01:06:03 8348191 reads; of these: 8348191 (100.00%) were paired; of these: 2126294 (25.47%) aligned concordantly 0 times 1606785 (19.25%) aligned concordantly exactly 1 time 4615112 (55.28%) aligned concordantly >1 times ---- 2126294 pairs aligned concordantly 0 times; of these: 278211 (13.08%) aligned discordantly 1 time ---- 1848083 pairs aligned 0 times concordantly or discordantly; of these: 3696166 mates make up the pairs; of these: 1719392 (46.52%) aligned 0 times 683576 (18.49%) aligned exactly 1 time 1293198 (34.99%) aligned >1 times 89.70% overall alignment rate Time searching: 01:06:03 Overall time: 01:06:03 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 12 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] 2006966 / 6300175 = 0.3186 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 @ Thu, 16 Apr 2020 05:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.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 @ Thu, 16 Apr 2020 05:49:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:49:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:49:44: 1000000 INFO @ Thu, 16 Apr 2020 05:49:52: 2000000 INFO @ Thu, 16 Apr 2020 05:50:00: 3000000 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 @ Thu, 16 Apr 2020 05:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.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 @ Thu, 16 Apr 2020 05:50:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:50:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:50:09: 4000000 INFO @ Thu, 16 Apr 2020 05:50:14: 1000000 INFO @ Thu, 16 Apr 2020 05:50:19: 5000000 INFO @ Thu, 16 Apr 2020 05:50:24: 2000000 INFO @ Thu, 16 Apr 2020 05:50:29: 6000000 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 @ Thu, 16 Apr 2020 05:50:33: 3000000 INFO @ Thu, 16 Apr 2020 05:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.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 @ Thu, 16 Apr 2020 05:50:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:50:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:50:38: 7000000 INFO @ Thu, 16 Apr 2020 05:50:43: 4000000 INFO @ Thu, 16 Apr 2020 05:50:45: 1000000 INFO @ Thu, 16 Apr 2020 05:50:48: 8000000 INFO @ Thu, 16 Apr 2020 05:50:52: 5000000 INFO @ Thu, 16 Apr 2020 05:50:55: 2000000 INFO @ Thu, 16 Apr 2020 05:50:57: 9000000 INFO @ Thu, 16 Apr 2020 05:51:02: 6000000 INFO @ Thu, 16 Apr 2020 05:51:04: 3000000 INFO @ Thu, 16 Apr 2020 05:51:07: 10000000 INFO @ Thu, 16 Apr 2020 05:51:12: 7000000 INFO @ Thu, 16 Apr 2020 05:51:14: 4000000 INFO @ Thu, 16 Apr 2020 05:51:16: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:51:16: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:51:16: #1 total tags in treatment: 4234495 INFO @ Thu, 16 Apr 2020 05:51:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:51:17: #1 tags after filtering in treatment: 3495686 INFO @ Thu, 16 Apr 2020 05:51:17: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 05:51:17: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:17: #2 number of paired peaks: 5420 INFO @ Thu, 16 Apr 2020 05:51:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:17: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:51:17: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05_model.r WARNING @ Thu, 16 Apr 2020 05:51:17: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:51:17: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 05:51:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:51:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:21: 8000000 INFO @ Thu, 16 Apr 2020 05:51:23: 5000000 INFO @ Thu, 16 Apr 2020 05:51:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:51:30: 9000000 INFO @ Thu, 16 Apr 2020 05:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.05_summits.bed INFO @ Thu, 16 Apr 2020 05:51:32: Done! INFO @ Thu, 16 Apr 2020 05:51:33: 6000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11948 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:51:40: 10000000 INFO @ Thu, 16 Apr 2020 05:51:42: 7000000 INFO @ Thu, 16 Apr 2020 05:51:49: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:51:49: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:51:49: #1 total tags in treatment: 4234495 INFO @ Thu, 16 Apr 2020 05:51:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:51:49: #1 tags after filtering in treatment: 3495686 INFO @ Thu, 16 Apr 2020 05:51:49: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 05:51:49: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:50: #2 number of paired peaks: 5420 INFO @ Thu, 16 Apr 2020 05:51:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:50: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:51:50: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10_model.r WARNING @ Thu, 16 Apr 2020 05:51:50: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:51:50: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 05:51:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:51:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:51: 8000000 INFO @ Thu, 16 Apr 2020 05:52:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:52:00: 9000000 INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.10_summits.bed INFO @ Thu, 16 Apr 2020 05:52:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6429 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:52:09: 10000000 INFO @ Thu, 16 Apr 2020 05:52:17: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:52:17: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:52:17: #1 total tags in treatment: 4234495 INFO @ Thu, 16 Apr 2020 05:52:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:52:17: #1 tags after filtering in treatment: 3495686 INFO @ Thu, 16 Apr 2020 05:52:17: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 16 Apr 2020 05:52:17: #1 finished! INFO @ Thu, 16 Apr 2020 05:52:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:52:17: #2 number of paired peaks: 5420 INFO @ Thu, 16 Apr 2020 05:52:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:52:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:52:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:52:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:52:17: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:52:17: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20_model.r WARNING @ Thu, 16 Apr 2020 05:52:17: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:52:17: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 05:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:52:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:52:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448079/SRX6448079.20_summits.bed INFO @ Thu, 16 Apr 2020 05:52:33: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2225 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。