Job ID = 5720773 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,153,788 reads read : 34,307,576 reads written : 34,307,576 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:50:19 17153788 reads; of these: 17153788 (100.00%) were paired; of these: 3517765 (20.51%) aligned concordantly 0 times 9787380 (57.06%) aligned concordantly exactly 1 time 3848643 (22.44%) aligned concordantly >1 times ---- 3517765 pairs aligned concordantly 0 times; of these: 1214062 (34.51%) aligned discordantly 1 time ---- 2303703 pairs aligned 0 times concordantly or discordantly; of these: 4607406 mates make up the pairs; of these: 2417076 (52.46%) aligned 0 times 1017002 (22.07%) aligned exactly 1 time 1173328 (25.47%) aligned >1 times 92.95% overall alignment rate Time searching: 00:50:20 Overall time: 00:50:20 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] 2187767 / 14337103 = 0.1526 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 02:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.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 02:37:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:37:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:38:05: 1000000 INFO @ Thu, 16 Apr 2020 02:38:13: 2000000 INFO @ Thu, 16 Apr 2020 02:38:20: 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 02:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.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 02:38:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:38:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:38:28: 4000000 INFO @ Thu, 16 Apr 2020 02:38:36: 1000000 INFO @ Thu, 16 Apr 2020 02:38:36: 5000000 INFO @ Thu, 16 Apr 2020 02:38:45: 2000000 INFO @ Thu, 16 Apr 2020 02:38:45: 6000000 INFO @ Thu, 16 Apr 2020 02:38:52: 3000000 INFO @ Thu, 16 Apr 2020 02:38:52: 7000000 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 02:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.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 02:38:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:38:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:39:00: 4000000 INFO @ Thu, 16 Apr 2020 02:39:00: 8000000 INFO @ Thu, 16 Apr 2020 02:39:03: 1000000 INFO @ Thu, 16 Apr 2020 02:39:08: 9000000 INFO @ Thu, 16 Apr 2020 02:39:08: 5000000 INFO @ Thu, 16 Apr 2020 02:39:10: 2000000 INFO @ Thu, 16 Apr 2020 02:39:15: 10000000 INFO @ Thu, 16 Apr 2020 02:39:15: 6000000 INFO @ Thu, 16 Apr 2020 02:39:17: 3000000 INFO @ Thu, 16 Apr 2020 02:39:23: 11000000 INFO @ Thu, 16 Apr 2020 02:39:23: 7000000 INFO @ Thu, 16 Apr 2020 02:39:23: 4000000 INFO @ Thu, 16 Apr 2020 02:39:30: 5000000 INFO @ Thu, 16 Apr 2020 02:39:31: 12000000 INFO @ Thu, 16 Apr 2020 02:39:31: 8000000 INFO @ Thu, 16 Apr 2020 02:39:37: 6000000 INFO @ Thu, 16 Apr 2020 02:39:39: 13000000 INFO @ Thu, 16 Apr 2020 02:39:39: 9000000 INFO @ Thu, 16 Apr 2020 02:39:43: 7000000 INFO @ Thu, 16 Apr 2020 02:39:46: 14000000 INFO @ Thu, 16 Apr 2020 02:39:46: 10000000 INFO @ Thu, 16 Apr 2020 02:39:50: 8000000 INFO @ Thu, 16 Apr 2020 02:39:53: 11000000 INFO @ Thu, 16 Apr 2020 02:39:54: 15000000 INFO @ Thu, 16 Apr 2020 02:39:56: 9000000 INFO @ Thu, 16 Apr 2020 02:40:01: 12000000 INFO @ Thu, 16 Apr 2020 02:40:01: 16000000 INFO @ Thu, 16 Apr 2020 02:40:03: 10000000 INFO @ Thu, 16 Apr 2020 02:40:08: 13000000 INFO @ Thu, 16 Apr 2020 02:40:09: 17000000 INFO @ Thu, 16 Apr 2020 02:40:09: 11000000 INFO @ Thu, 16 Apr 2020 02:40:15: 14000000 INFO @ Thu, 16 Apr 2020 02:40:16: 12000000 INFO @ Thu, 16 Apr 2020 02:40:17: 18000000 INFO @ Thu, 16 Apr 2020 02:40:22: 15000000 INFO @ Thu, 16 Apr 2020 02:40:23: 13000000 INFO @ Thu, 16 Apr 2020 02:40:24: 19000000 INFO @ Thu, 16 Apr 2020 02:40:29: 16000000 INFO @ Thu, 16 Apr 2020 02:40:29: 14000000 INFO @ Thu, 16 Apr 2020 02:40:32: 20000000 INFO @ Thu, 16 Apr 2020 02:40:36: 15000000 INFO @ Thu, 16 Apr 2020 02:40:37: 17000000 INFO @ Thu, 16 Apr 2020 02:40:40: 21000000 INFO @ Thu, 16 Apr 2020 02:40:42: 16000000 INFO @ Thu, 16 Apr 2020 02:40:45: 18000000 INFO @ Thu, 16 Apr 2020 02:40:48: 22000000 INFO @ Thu, 16 Apr 2020 02:40:49: 17000000 INFO @ Thu, 16 Apr 2020 02:40:52: 19000000 INFO @ Thu, 16 Apr 2020 02:40:55: 18000000 INFO @ Thu, 16 Apr 2020 02:40:56: 23000000 INFO @ Thu, 16 Apr 2020 02:41:00: 20000000 INFO @ Thu, 16 Apr 2020 02:41:01: 19000000 INFO @ Thu, 16 Apr 2020 02:41:04: 24000000 INFO @ Thu, 16 Apr 2020 02:41:08: 20000000 INFO @ Thu, 16 Apr 2020 02:41:08: 21000000 INFO @ Thu, 16 Apr 2020 02:41:12: 25000000 INFO @ Thu, 16 Apr 2020 02:41:15: 21000000 INFO @ Thu, 16 Apr 2020 02:41:16: 22000000 INFO @ Thu, 16 Apr 2020 02:41:20: 26000000 INFO @ Thu, 16 Apr 2020 02:41:22: 22000000 INFO @ Thu, 16 Apr 2020 02:41:24: 23000000 INFO @ Thu, 16 Apr 2020 02:41:28: 27000000 INFO @ Thu, 16 Apr 2020 02:41:28: 23000000 INFO @ Thu, 16 Apr 2020 02:41:32: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:41:32: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:41:32: #1 total tags in treatment: 11536151 INFO @ Thu, 16 Apr 2020 02:41:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:41:32: #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 02:41:32: #1 tags after filtering in treatment: 11056810 INFO @ Thu, 16 Apr 2020 02:41:32: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:41:32: #1 finished! INFO @ Thu, 16 Apr 2020 02:41:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:41:32: 24000000 INFO @ Thu, 16 Apr 2020 02:41:33: #2 number of paired peaks: 183 WARNING @ Thu, 16 Apr 2020 02:41:33: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 16 Apr 2020 02:41:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:41:33: start X-correlation... INFO @ Thu, 16 Apr 2020 02:41:33: end of X-cor INFO @ Thu, 16 Apr 2020 02:41:33: #2 finished! INFO @ Thu, 16 Apr 2020 02:41:33: #2 predicted fragment length is 152 bps INFO @ Thu, 16 Apr 2020 02:41:33: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 16 Apr 2020 02:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05_model.r WARNING @ Thu, 16 Apr 2020 02:41:33: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:41:33: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Thu, 16 Apr 2020 02:41:33: #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 02:41:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:41:35: 24000000 INFO @ Thu, 16 Apr 2020 02:41:40: 25000000 INFO @ Thu, 16 Apr 2020 02:41:42: 25000000 INFO @ Thu, 16 Apr 2020 02:41:48: 26000000 INFO @ Thu, 16 Apr 2020 02:41:49: 26000000 INFO @ Thu, 16 Apr 2020 02:41:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:41:56: 27000000 INFO @ Thu, 16 Apr 2020 02:41:56: 27000000 INFO @ Thu, 16 Apr 2020 02:42:00: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:42:00: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:42:00: #1 total tags in treatment: 11536151 INFO @ Thu, 16 Apr 2020 02:42:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:42:00: #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 02:42:00: #1 tags after filtering in treatment: 11056810 INFO @ Thu, 16 Apr 2020 02:42:00: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:42:00: #1 finished! INFO @ Thu, 16 Apr 2020 02:42:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:42:00: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:42:00: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:42:00: #1 total tags in treatment: 11536151 INFO @ Thu, 16 Apr 2020 02:42:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:42:00: #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 02:42:01: #1 tags after filtering in treatment: 11056810 INFO @ Thu, 16 Apr 2020 02:42:01: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:42:01: #1 finished! INFO @ Thu, 16 Apr 2020 02:42:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:42:01: #2 number of paired peaks: 183 WARNING @ Thu, 16 Apr 2020 02:42:01: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 16 Apr 2020 02:42:01: start model_add_line... INFO @ Thu, 16 Apr 2020 02:42:01: start X-correlation... INFO @ Thu, 16 Apr 2020 02:42:01: end of X-cor INFO @ Thu, 16 Apr 2020 02:42:01: #2 finished! INFO @ Thu, 16 Apr 2020 02:42:01: #2 predicted fragment length is 152 bps INFO @ Thu, 16 Apr 2020 02:42:01: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 16 Apr 2020 02:42:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10_model.r WARNING @ Thu, 16 Apr 2020 02:42:01: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:42:01: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Thu, 16 Apr 2020 02:42:01: #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 02:42:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:42:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:42:01: #2 number of paired peaks: 183 WARNING @ Thu, 16 Apr 2020 02:42:01: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 16 Apr 2020 02:42:01: start model_add_line... INFO @ Thu, 16 Apr 2020 02:42:01: start X-correlation... INFO @ Thu, 16 Apr 2020 02:42:01: end of X-cor INFO @ Thu, 16 Apr 2020 02:42:01: #2 finished! INFO @ Thu, 16 Apr 2020 02:42:01: #2 predicted fragment length is 152 bps INFO @ Thu, 16 Apr 2020 02:42:01: #2 alternative fragment length(s) may be 152 bps INFO @ Thu, 16 Apr 2020 02:42:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20_model.r WARNING @ Thu, 16 Apr 2020 02:42:01: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:42:01: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Thu, 16 Apr 2020 02:42:01: #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 02:42:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:42:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.05_summits.bed INFO @ Thu, 16 Apr 2020 02:42:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2854 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:42:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:42:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.10_summits.bed INFO @ Thu, 16 Apr 2020 02:42:33: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1026 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246866/SRX5246866.20_summits.bed INFO @ Thu, 16 Apr 2020 02:42:34: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。