Job ID = 5721111 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,589,691 reads read : 15,179,382 reads written : 15,179,382 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: 00:12:48 7589691 reads; of these: 7589691 (100.00%) were paired; of these: 874024 (11.52%) aligned concordantly 0 times 5359257 (70.61%) aligned concordantly exactly 1 time 1356410 (17.87%) aligned concordantly >1 times ---- 874024 pairs aligned concordantly 0 times; of these: 265403 (30.37%) aligned discordantly 1 time ---- 608621 pairs aligned 0 times concordantly or discordantly; of these: 1217242 mates make up the pairs; of these: 780291 (64.10%) aligned 0 times 212812 (17.48%) aligned exactly 1 time 224139 (18.41%) aligned >1 times 94.86% overall alignment rate Time searching: 00:12:48 Overall time: 00:12:48 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] 488833 / 6961980 = 0.0702 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 05:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.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 05:08:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:29: 1000000 INFO @ Thu, 16 Apr 2020 05:08:34: 2000000 INFO @ Thu, 16 Apr 2020 05:08:39: 3000000 INFO @ Thu, 16 Apr 2020 05:08:44: 4000000 INFO @ Thu, 16 Apr 2020 05:08:49: 5000000 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 05:08:54: 6000000 INFO @ Thu, 16 Apr 2020 05:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.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 05:08:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:59: 7000000 INFO @ Thu, 16 Apr 2020 05:08:59: 1000000 INFO @ Thu, 16 Apr 2020 05:09:04: 8000000 INFO @ Thu, 16 Apr 2020 05:09:04: 2000000 INFO @ Thu, 16 Apr 2020 05:09:09: 9000000 INFO @ Thu, 16 Apr 2020 05:09:10: 3000000 INFO @ Thu, 16 Apr 2020 05:09:14: 10000000 INFO @ Thu, 16 Apr 2020 05:09:15: 4000000 INFO @ Thu, 16 Apr 2020 05:09:19: 11000000 INFO @ Thu, 16 Apr 2020 05:09:20: 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 @ Thu, 16 Apr 2020 05:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.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 05:09:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:24: 12000000 INFO @ Thu, 16 Apr 2020 05:09:25: 6000000 INFO @ Thu, 16 Apr 2020 05:09:29: 1000000 INFO @ Thu, 16 Apr 2020 05:09:29: 13000000 INFO @ Thu, 16 Apr 2020 05:09:31: 7000000 INFO @ Thu, 16 Apr 2020 05:09:32: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:09:32: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:09:32: #1 total tags in treatment: 6242027 INFO @ Thu, 16 Apr 2020 05:09:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:32: #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 05:09:32: #1 tags after filtering in treatment: 5913430 INFO @ Thu, 16 Apr 2020 05:09:32: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:09:32: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:32: #2 number of paired peaks: 458 WARNING @ Thu, 16 Apr 2020 05:09:32: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Thu, 16 Apr 2020 05:09:32: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:32: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:32: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:32: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:32: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:09:32: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05_model.r INFO @ Thu, 16 Apr 2020 05:09:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:35: 2000000 INFO @ Thu, 16 Apr 2020 05:09:36: 8000000 INFO @ Thu, 16 Apr 2020 05:09:40: 3000000 INFO @ Thu, 16 Apr 2020 05:09:41: 9000000 INFO @ Thu, 16 Apr 2020 05:09:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:45: 4000000 INFO @ Thu, 16 Apr 2020 05:09:46: 10000000 INFO @ Thu, 16 Apr 2020 05:09:51: 5000000 INFO @ Thu, 16 Apr 2020 05:09:52: 11000000 INFO @ Thu, 16 Apr 2020 05:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.05_summits.bed INFO @ Thu, 16 Apr 2020 05:09:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:09:56: 6000000 INFO @ Thu, 16 Apr 2020 05:09:57: 12000000 INFO @ Thu, 16 Apr 2020 05:10:02: 7000000 INFO @ Thu, 16 Apr 2020 05:10:02: 13000000 INFO @ Thu, 16 Apr 2020 05:10:04: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:04: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:04: #1 total tags in treatment: 6242027 INFO @ Thu, 16 Apr 2020 05:10:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:04: #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 05:10:05: #1 tags after filtering in treatment: 5913430 INFO @ Thu, 16 Apr 2020 05:10:05: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:10:05: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:05: #2 number of paired peaks: 458 WARNING @ Thu, 16 Apr 2020 05:10:05: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:05: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:05: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:05: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:05: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:05: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:10:05: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10_model.r INFO @ Thu, 16 Apr 2020 05:10:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:07: 8000000 INFO @ Thu, 16 Apr 2020 05:10:13: 9000000 INFO @ Thu, 16 Apr 2020 05:10:18: 10000000 INFO @ Thu, 16 Apr 2020 05:10:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:23: 11000000 INFO @ Thu, 16 Apr 2020 05:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.10_summits.bed INFO @ Thu, 16 Apr 2020 05:10:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:29: 12000000 INFO @ Thu, 16 Apr 2020 05:10:35: 13000000 INFO @ Thu, 16 Apr 2020 05:10:37: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:37: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:37: #1 total tags in treatment: 6242027 INFO @ Thu, 16 Apr 2020 05:10:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:37: #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 05:10:37: #1 tags after filtering in treatment: 5913430 INFO @ Thu, 16 Apr 2020 05:10:37: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:10:37: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:37: #2 number of paired peaks: 458 WARNING @ Thu, 16 Apr 2020 05:10:37: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:37: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:38: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:38: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:38: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:38: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 05:10:38: #2 alternative fragment length(s) may be 196 bps INFO @ Thu, 16 Apr 2020 05:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20_model.r INFO @ Thu, 16 Apr 2020 05:10:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708255/SRX6708255.20_summits.bed INFO @ Thu, 16 Apr 2020 05:10:58: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (326 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。