Job ID = 5721113 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,684,430 reads read : 13,368,860 reads written : 13,368,860 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: 00:10:12 6684430 reads; of these: 6684430 (100.00%) were paired; of these: 959138 (14.35%) aligned concordantly 0 times 4565443 (68.30%) aligned concordantly exactly 1 time 1159849 (17.35%) aligned concordantly >1 times ---- 959138 pairs aligned concordantly 0 times; of these: 280196 (29.21%) aligned discordantly 1 time ---- 678942 pairs aligned 0 times concordantly or discordantly; of these: 1357884 mates make up the pairs; of these: 901703 (66.41%) aligned 0 times 215856 (15.90%) aligned exactly 1 time 240325 (17.70%) aligned >1 times 93.26% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 429759 / 5987190 = 0.0718 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 05:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.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 05:07:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:07:51: 1000000 INFO @ Thu, 16 Apr 2020 05:07:58: 2000000 INFO @ Thu, 16 Apr 2020 05:08:04: 3000000 INFO @ Thu, 16 Apr 2020 05:08:10: 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 05:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.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 05:08:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:16: 5000000 INFO @ Thu, 16 Apr 2020 05:08:22: 1000000 INFO @ Thu, 16 Apr 2020 05:08:22: 6000000 INFO @ Thu, 16 Apr 2020 05:08:27: 2000000 INFO @ Thu, 16 Apr 2020 05:08:28: 7000000 INFO @ Thu, 16 Apr 2020 05:08:33: 3000000 INFO @ Thu, 16 Apr 2020 05:08:34: 8000000 INFO @ Thu, 16 Apr 2020 05:08:39: 4000000 INFO @ Thu, 16 Apr 2020 05:08:40: 9000000 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 05:08:45: 5000000 INFO @ Thu, 16 Apr 2020 05:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.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 05:08:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:47: 10000000 INFO @ Thu, 16 Apr 2020 05:08:51: 6000000 INFO @ Thu, 16 Apr 2020 05:08:51: 1000000 INFO @ Thu, 16 Apr 2020 05:08:53: 11000000 INFO @ Thu, 16 Apr 2020 05:08:56: 7000000 INFO @ Thu, 16 Apr 2020 05:08:57: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:08:57: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:08:57: #1 total tags in treatment: 5311554 INFO @ Thu, 16 Apr 2020 05:08:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:08:57: #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 05:08:57: #1 tags after filtering in treatment: 5019448 INFO @ Thu, 16 Apr 2020 05:08:57: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:08:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:08:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:08:57: 2000000 INFO @ Thu, 16 Apr 2020 05:08:57: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:08:57: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:08:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:08:57: start X-correlation... INFO @ Thu, 16 Apr 2020 05:08:57: end of X-cor INFO @ Thu, 16 Apr 2020 05:08:57: #2 finished! INFO @ Thu, 16 Apr 2020 05:08:57: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:08:57: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05_model.r INFO @ Thu, 16 Apr 2020 05:08:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:02: 8000000 INFO @ Thu, 16 Apr 2020 05:09:03: 3000000 INFO @ Thu, 16 Apr 2020 05:09:07: 9000000 INFO @ Thu, 16 Apr 2020 05:09:08: 4000000 INFO @ Thu, 16 Apr 2020 05:09:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:13: 10000000 INFO @ Thu, 16 Apr 2020 05:09:13: 5000000 INFO @ Thu, 16 Apr 2020 05:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.05_summits.bed INFO @ Thu, 16 Apr 2020 05:09:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2512 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:09:18: 11000000 INFO @ Thu, 16 Apr 2020 05:09:19: 6000000 INFO @ Thu, 16 Apr 2020 05:09:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:09:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:09:22: #1 total tags in treatment: 5311554 INFO @ Thu, 16 Apr 2020 05:09:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:22: #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 05:09:22: #1 tags after filtering in treatment: 5019448 INFO @ Thu, 16 Apr 2020 05:09:22: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:09:22: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:22: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:09:22: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:09:22: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:22: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:22: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:22: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:22: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:09:22: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:09:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10_model.r INFO @ Thu, 16 Apr 2020 05:09:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:24: 7000000 INFO @ Thu, 16 Apr 2020 05:09:30: 8000000 INFO @ Thu, 16 Apr 2020 05:09:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:35: 9000000 INFO @ Thu, 16 Apr 2020 05:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.10_summits.bed INFO @ Thu, 16 Apr 2020 05:09:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:09:40: 10000000 INFO @ Thu, 16 Apr 2020 05:09:45: 11000000 INFO @ Thu, 16 Apr 2020 05:09:49: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:09:49: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:09:49: #1 total tags in treatment: 5311554 INFO @ Thu, 16 Apr 2020 05:09:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:49: #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 05:09:49: #1 tags after filtering in treatment: 5019448 INFO @ Thu, 16 Apr 2020 05:09:49: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:09:49: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:49: #2 number of paired peaks: 688 WARNING @ Thu, 16 Apr 2020 05:09:49: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Thu, 16 Apr 2020 05:09:49: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:49: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:49: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:49: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:49: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:09:49: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20_model.r INFO @ Thu, 16 Apr 2020 05:09:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708257/SRX6708257.20_summits.bed INFO @ Thu, 16 Apr 2020 05:10:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (421 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。