Job ID = 5721145 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,481,147 reads read : 20,962,294 reads written : 20,962,294 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: 00:21:24 10481147 reads; of these: 10481147 (100.00%) were paired; of these: 2412668 (23.02%) aligned concordantly 0 times 5572660 (53.17%) aligned concordantly exactly 1 time 2495819 (23.81%) aligned concordantly >1 times ---- 2412668 pairs aligned concordantly 0 times; of these: 79110 (3.28%) aligned discordantly 1 time ---- 2333558 pairs aligned 0 times concordantly or discordantly; of these: 4667116 mates make up the pairs; of these: 4322918 (92.63%) aligned 0 times 196268 (4.21%) aligned exactly 1 time 147930 (3.17%) aligned >1 times 79.38% overall alignment rate Time searching: 00:21:24 Overall time: 00:21:24 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 8 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] 437264 / 8129174 = 0.0538 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 05:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.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 05:48:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:48:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:49:05: 1000000 INFO @ Thu, 16 Apr 2020 05:49:11: 2000000 INFO @ Thu, 16 Apr 2020 05:49:17: 3000000 INFO @ Thu, 16 Apr 2020 05:49:22: 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 05:49:28: 5000000 INFO @ Thu, 16 Apr 2020 05:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.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 05:49:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:49:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:49:34: 6000000 INFO @ Thu, 16 Apr 2020 05:49:35: 1000000 INFO @ Thu, 16 Apr 2020 05:49:41: 7000000 INFO @ Thu, 16 Apr 2020 05:49:41: 2000000 INFO @ Thu, 16 Apr 2020 05:49:47: 8000000 INFO @ Thu, 16 Apr 2020 05:49:48: 3000000 INFO @ Thu, 16 Apr 2020 05:49:54: 9000000 INFO @ Thu, 16 Apr 2020 05:49:54: 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 05:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.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 05:49:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:49:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:50:00: 10000000 INFO @ Thu, 16 Apr 2020 05:50:01: 5000000 INFO @ Thu, 16 Apr 2020 05:50:05: 1000000 INFO @ Thu, 16 Apr 2020 05:50:07: 11000000 INFO @ Thu, 16 Apr 2020 05:50:07: 6000000 INFO @ Thu, 16 Apr 2020 05:50:12: 2000000 INFO @ Thu, 16 Apr 2020 05:50:13: 12000000 INFO @ Thu, 16 Apr 2020 05:50:14: 7000000 INFO @ Thu, 16 Apr 2020 05:50:19: 3000000 INFO @ Thu, 16 Apr 2020 05:50:20: 13000000 INFO @ Thu, 16 Apr 2020 05:50:20: 8000000 INFO @ Thu, 16 Apr 2020 05:50:25: 4000000 INFO @ Thu, 16 Apr 2020 05:50:27: 14000000 INFO @ Thu, 16 Apr 2020 05:50:27: 9000000 INFO @ Thu, 16 Apr 2020 05:50:32: 5000000 INFO @ Thu, 16 Apr 2020 05:50:33: 10000000 INFO @ Thu, 16 Apr 2020 05:50:33: 15000000 INFO @ Thu, 16 Apr 2020 05:50:38: 6000000 INFO @ Thu, 16 Apr 2020 05:50:38: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:50:38: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:50:38: #1 total tags in treatment: 7632225 INFO @ Thu, 16 Apr 2020 05:50:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:50:38: #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 05:50:39: #1 tags after filtering in treatment: 7319470 INFO @ Thu, 16 Apr 2020 05:50:39: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:50:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:50:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:50:39: #2 number of paired peaks: 987 WARNING @ Thu, 16 Apr 2020 05:50:39: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Thu, 16 Apr 2020 05:50:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:50:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:50:39: end of X-cor INFO @ Thu, 16 Apr 2020 05:50:39: #2 finished! INFO @ Thu, 16 Apr 2020 05:50:39: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 05:50:39: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 05:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05_model.r INFO @ Thu, 16 Apr 2020 05:50:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:50:40: 11000000 INFO @ Thu, 16 Apr 2020 05:50:45: 7000000 INFO @ Thu, 16 Apr 2020 05:50:47: 12000000 INFO @ Thu, 16 Apr 2020 05:50:52: 8000000 INFO @ Thu, 16 Apr 2020 05:50:53: 13000000 INFO @ Thu, 16 Apr 2020 05:50:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:50:58: 9000000 INFO @ Thu, 16 Apr 2020 05:51:00: 14000000 INFO @ Thu, 16 Apr 2020 05:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.05_summits.bed INFO @ Thu, 16 Apr 2020 05:51:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1786 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:51:05: 10000000 INFO @ Thu, 16 Apr 2020 05:51:06: 15000000 INFO @ Thu, 16 Apr 2020 05:51:11: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:51:11: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:51:11: #1 total tags in treatment: 7632225 INFO @ Thu, 16 Apr 2020 05:51:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:11: #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 05:51:11: 11000000 INFO @ Thu, 16 Apr 2020 05:51:11: #1 tags after filtering in treatment: 7319470 INFO @ Thu, 16 Apr 2020 05:51:11: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:51:11: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:12: #2 number of paired peaks: 987 WARNING @ Thu, 16 Apr 2020 05:51:12: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Thu, 16 Apr 2020 05:51:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:12: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 05:51:12: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 05:51:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10_model.r INFO @ Thu, 16 Apr 2020 05:51:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:17: 12000000 INFO @ Thu, 16 Apr 2020 05:51:23: 13000000 INFO @ Thu, 16 Apr 2020 05:51:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:51:29: 14000000 INFO @ Thu, 16 Apr 2020 05:51:35: 15000000 INFO @ Thu, 16 Apr 2020 05:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.10_summits.bed INFO @ Thu, 16 Apr 2020 05:51:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1038 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:51:39: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:51:39: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:51:39: #1 total tags in treatment: 7632225 INFO @ Thu, 16 Apr 2020 05:51:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:39: #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 05:51:39: #1 tags after filtering in treatment: 7319470 INFO @ Thu, 16 Apr 2020 05:51:39: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:51:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:40: #2 number of paired peaks: 987 WARNING @ Thu, 16 Apr 2020 05:51:40: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Thu, 16 Apr 2020 05:51:40: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:40: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:40: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:40: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:40: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 05:51:40: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 05:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20_model.r INFO @ Thu, 16 Apr 2020 05:51:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708283/SRX6708283.20_summits.bed INFO @ Thu, 16 Apr 2020 05:52:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (525 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。