Job ID = 5721225 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,852,606 reads read : 43,705,212 reads written : 43,705,212 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: 01:08:10 21852606 reads; of these: 21852606 (100.00%) were paired; of these: 2076891 (9.50%) aligned concordantly 0 times 14690069 (67.22%) aligned concordantly exactly 1 time 5085646 (23.27%) aligned concordantly >1 times ---- 2076891 pairs aligned concordantly 0 times; of these: 620310 (29.87%) aligned discordantly 1 time ---- 1456581 pairs aligned 0 times concordantly or discordantly; of these: 2913162 mates make up the pairs; of these: 1745461 (59.92%) aligned 0 times 398378 (13.68%) aligned exactly 1 time 769323 (26.41%) aligned >1 times 96.01% overall alignment rate Time searching: 01:08:10 Overall time: 01:08:10 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 20 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] 2894717 / 20339761 = 0.1423 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 07:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.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 07:35:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:35:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:35:20: 1000000 INFO @ Thu, 16 Apr 2020 07:35:26: 2000000 INFO @ Thu, 16 Apr 2020 07:35:33: 3000000 INFO @ Thu, 16 Apr 2020 07:35:39: 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 @ Thu, 16 Apr 2020 07:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.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 07:35:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:35:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:35:46: 5000000 INFO @ Thu, 16 Apr 2020 07:35:49: 1000000 INFO @ Thu, 16 Apr 2020 07:35:53: 6000000 INFO @ Thu, 16 Apr 2020 07:35:55: 2000000 INFO @ Thu, 16 Apr 2020 07:36:00: 7000000 INFO @ Thu, 16 Apr 2020 07:36:02: 3000000 INFO @ Thu, 16 Apr 2020 07:36:06: 8000000 INFO @ Thu, 16 Apr 2020 07:36:08: 4000000 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 07:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.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 07:36:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:36:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:36:13: 9000000 INFO @ Thu, 16 Apr 2020 07:36:14: 5000000 INFO @ Thu, 16 Apr 2020 07:36:20: 6000000 INFO @ Thu, 16 Apr 2020 07:36:20: 1000000 INFO @ Thu, 16 Apr 2020 07:36:21: 10000000 INFO @ Thu, 16 Apr 2020 07:36:26: 7000000 INFO @ Thu, 16 Apr 2020 07:36:28: 2000000 INFO @ Thu, 16 Apr 2020 07:36:28: 11000000 INFO @ Thu, 16 Apr 2020 07:36:32: 8000000 INFO @ Thu, 16 Apr 2020 07:36:35: 3000000 INFO @ Thu, 16 Apr 2020 07:36:36: 12000000 INFO @ Thu, 16 Apr 2020 07:36:39: 9000000 INFO @ Thu, 16 Apr 2020 07:36:43: 4000000 INFO @ Thu, 16 Apr 2020 07:36:44: 13000000 INFO @ Thu, 16 Apr 2020 07:36:45: 10000000 INFO @ Thu, 16 Apr 2020 07:36:51: 11000000 INFO @ Thu, 16 Apr 2020 07:36:51: 5000000 INFO @ Thu, 16 Apr 2020 07:36:51: 14000000 INFO @ Thu, 16 Apr 2020 07:36:57: 12000000 INFO @ Thu, 16 Apr 2020 07:36:59: 6000000 INFO @ Thu, 16 Apr 2020 07:36:59: 15000000 INFO @ Thu, 16 Apr 2020 07:37:03: 13000000 INFO @ Thu, 16 Apr 2020 07:37:06: 16000000 INFO @ Thu, 16 Apr 2020 07:37:06: 7000000 INFO @ Thu, 16 Apr 2020 07:37:09: 14000000 INFO @ Thu, 16 Apr 2020 07:37:13: 17000000 INFO @ Thu, 16 Apr 2020 07:37:14: 8000000 INFO @ Thu, 16 Apr 2020 07:37:16: 15000000 INFO @ Thu, 16 Apr 2020 07:37:20: 18000000 INFO @ Thu, 16 Apr 2020 07:37:21: 9000000 INFO @ Thu, 16 Apr 2020 07:37:22: 16000000 INFO @ Thu, 16 Apr 2020 07:37:27: 19000000 INFO @ Thu, 16 Apr 2020 07:37:28: 17000000 INFO @ Thu, 16 Apr 2020 07:37:28: 10000000 INFO @ Thu, 16 Apr 2020 07:37:34: 20000000 INFO @ Thu, 16 Apr 2020 07:37:34: 18000000 INFO @ Thu, 16 Apr 2020 07:37:36: 11000000 INFO @ Thu, 16 Apr 2020 07:37:40: 19000000 INFO @ Thu, 16 Apr 2020 07:37:40: 21000000 INFO @ Thu, 16 Apr 2020 07:37:43: 12000000 INFO @ Thu, 16 Apr 2020 07:37:46: 20000000 INFO @ Thu, 16 Apr 2020 07:37:47: 22000000 INFO @ Thu, 16 Apr 2020 07:37:51: 13000000 INFO @ Thu, 16 Apr 2020 07:37:53: 21000000 INFO @ Thu, 16 Apr 2020 07:37:55: 23000000 INFO @ Thu, 16 Apr 2020 07:37:58: 14000000 INFO @ Thu, 16 Apr 2020 07:37:59: 22000000 INFO @ Thu, 16 Apr 2020 07:38:02: 24000000 INFO @ Thu, 16 Apr 2020 07:38:05: 23000000 INFO @ Thu, 16 Apr 2020 07:38:06: 15000000 INFO @ Thu, 16 Apr 2020 07:38:10: 25000000 INFO @ Thu, 16 Apr 2020 07:38:11: 24000000 INFO @ Thu, 16 Apr 2020 07:38:13: 16000000 INFO @ Thu, 16 Apr 2020 07:38:17: 25000000 INFO @ Thu, 16 Apr 2020 07:38:17: 26000000 INFO @ Thu, 16 Apr 2020 07:38:21: 17000000 INFO @ Thu, 16 Apr 2020 07:38:23: 26000000 INFO @ Thu, 16 Apr 2020 07:38:25: 27000000 INFO @ Thu, 16 Apr 2020 07:38:28: 18000000 INFO @ Thu, 16 Apr 2020 07:38:29: 27000000 INFO @ Thu, 16 Apr 2020 07:38:32: 28000000 INFO @ Thu, 16 Apr 2020 07:38:35: 28000000 INFO @ Thu, 16 Apr 2020 07:38:36: 19000000 INFO @ Thu, 16 Apr 2020 07:38:40: 29000000 INFO @ Thu, 16 Apr 2020 07:38:41: 29000000 INFO @ Thu, 16 Apr 2020 07:38:43: 20000000 INFO @ Thu, 16 Apr 2020 07:38:47: 30000000 INFO @ Thu, 16 Apr 2020 07:38:48: 30000000 INFO @ Thu, 16 Apr 2020 07:38:51: 21000000 INFO @ Thu, 16 Apr 2020 07:38:54: 31000000 INFO @ Thu, 16 Apr 2020 07:38:55: 31000000 INFO @ Thu, 16 Apr 2020 07:38:58: 22000000 INFO @ Thu, 16 Apr 2020 07:39:02: 32000000 INFO @ Thu, 16 Apr 2020 07:39:02: 32000000 INFO @ Thu, 16 Apr 2020 07:39:06: 23000000 INFO @ Thu, 16 Apr 2020 07:39:09: 33000000 INFO @ Thu, 16 Apr 2020 07:39:10: 33000000 INFO @ Thu, 16 Apr 2020 07:39:13: 24000000 INFO @ Thu, 16 Apr 2020 07:39:17: 34000000 INFO @ Thu, 16 Apr 2020 07:39:17: 34000000 INFO @ Thu, 16 Apr 2020 07:39:21: 25000000 INFO @ Thu, 16 Apr 2020 07:39:24: 35000000 INFO @ Thu, 16 Apr 2020 07:39:24: 35000000 INFO @ Thu, 16 Apr 2020 07:39:28: 26000000 INFO @ Thu, 16 Apr 2020 07:39:31: 36000000 INFO @ Thu, 16 Apr 2020 07:39:32: 36000000 INFO @ Thu, 16 Apr 2020 07:39:33: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 07:39:33: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 07:39:33: #1 total tags in treatment: 16970980 INFO @ Thu, 16 Apr 2020 07:39:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:39:33: #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 07:39:33: #1 tags after filtering in treatment: 15752725 INFO @ Thu, 16 Apr 2020 07:39:33: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 07:39:33: #1 finished! INFO @ Thu, 16 Apr 2020 07:39:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:39:33: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 07:39:33: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 07:39:33: #1 total tags in treatment: 16970980 INFO @ Thu, 16 Apr 2020 07:39:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:39:33: #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 07:39:34: #1 tags after filtering in treatment: 15752725 INFO @ Thu, 16 Apr 2020 07:39:34: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 07:39:34: #1 finished! INFO @ Thu, 16 Apr 2020 07:39:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:39:34: #2 number of paired peaks: 744 WARNING @ Thu, 16 Apr 2020 07:39:34: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Thu, 16 Apr 2020 07:39:34: start model_add_line... INFO @ Thu, 16 Apr 2020 07:39:34: start X-correlation... INFO @ Thu, 16 Apr 2020 07:39:34: end of X-cor INFO @ Thu, 16 Apr 2020 07:39:34: #2 finished! INFO @ Thu, 16 Apr 2020 07:39:34: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 07:39:34: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 07:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05_model.r WARNING @ Thu, 16 Apr 2020 07:39:34: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:39:34: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 07:39:34: #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 07:39:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:39:35: #2 number of paired peaks: 744 WARNING @ Thu, 16 Apr 2020 07:39:35: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Thu, 16 Apr 2020 07:39:35: start model_add_line... INFO @ Thu, 16 Apr 2020 07:39:35: start X-correlation... INFO @ Thu, 16 Apr 2020 07:39:35: end of X-cor INFO @ Thu, 16 Apr 2020 07:39:35: #2 finished! INFO @ Thu, 16 Apr 2020 07:39:35: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 07:39:35: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 07:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10_model.r WARNING @ Thu, 16 Apr 2020 07:39:35: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:39:35: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 07:39:35: #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 07:39:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:39:35: 27000000 INFO @ Thu, 16 Apr 2020 07:39:42: 28000000 INFO @ Thu, 16 Apr 2020 07:39:49: 29000000 INFO @ Thu, 16 Apr 2020 07:39:56: 30000000 INFO @ Thu, 16 Apr 2020 07:40:03: 31000000 INFO @ Thu, 16 Apr 2020 07:40:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:40:10: 32000000 INFO @ Thu, 16 Apr 2020 07:40:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:40:17: 33000000 INFO @ Thu, 16 Apr 2020 07:40:23: 34000000 INFO @ Thu, 16 Apr 2020 07:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05_peaks.xls INFO @ Thu, 16 Apr 2020 07:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.05_summits.bed INFO @ Thu, 16 Apr 2020 07:40:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3441 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10_peaks.xls INFO @ Thu, 16 Apr 2020 07:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.10_summits.bed INFO @ Thu, 16 Apr 2020 07:40:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1932 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:40:30: 35000000 INFO @ Thu, 16 Apr 2020 07:40:36: 36000000 INFO @ Thu, 16 Apr 2020 07:40:38: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 07:40:38: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 07:40:38: #1 total tags in treatment: 16970980 INFO @ Thu, 16 Apr 2020 07:40:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:40:38: #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 07:40:38: #1 tags after filtering in treatment: 15752725 INFO @ Thu, 16 Apr 2020 07:40:38: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 07:40:38: #1 finished! INFO @ Thu, 16 Apr 2020 07:40:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:40:39: #2 number of paired peaks: 744 WARNING @ Thu, 16 Apr 2020 07:40:39: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Thu, 16 Apr 2020 07:40:39: start model_add_line... INFO @ Thu, 16 Apr 2020 07:40:39: start X-correlation... INFO @ Thu, 16 Apr 2020 07:40:39: end of X-cor INFO @ Thu, 16 Apr 2020 07:40:39: #2 finished! INFO @ Thu, 16 Apr 2020 07:40:39: #2 predicted fragment length is 202 bps INFO @ Thu, 16 Apr 2020 07:40:39: #2 alternative fragment length(s) may be 202 bps INFO @ Thu, 16 Apr 2020 07:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20_model.r WARNING @ Thu, 16 Apr 2020 07:40:39: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:40:39: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Thu, 16 Apr 2020 07:40:39: #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 07:40:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:41:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20_peaks.xls INFO @ Thu, 16 Apr 2020 07:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845081/SRX6845081.20_summits.bed INFO @ Thu, 16 Apr 2020 07:41:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。