Job ID = 5721098 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,503,123 reads read : 21,006,246 reads written : 21,006,246 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: 00:22:05 10503123 reads; of these: 10503123 (100.00%) were paired; of these: 881547 (8.39%) aligned concordantly 0 times 6850109 (65.22%) aligned concordantly exactly 1 time 2771467 (26.39%) aligned concordantly >1 times ---- 881547 pairs aligned concordantly 0 times; of these: 291374 (33.05%) aligned discordantly 1 time ---- 590173 pairs aligned 0 times concordantly or discordantly; of these: 1180346 mates make up the pairs; of these: 658031 (55.75%) aligned 0 times 269976 (22.87%) aligned exactly 1 time 252339 (21.38%) aligned >1 times 96.87% overall alignment rate Time searching: 00:22:06 Overall time: 00:22:06 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 12 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] 866157 / 9851850 = 0.0879 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 05:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.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 05:07:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:02: 1000000 INFO @ Thu, 16 Apr 2020 05:08:08: 2000000 INFO @ Thu, 16 Apr 2020 05:08:14: 3000000 INFO @ Thu, 16 Apr 2020 05:08:19: 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 05:08:25: 5000000 INFO @ Thu, 16 Apr 2020 05:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.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 05:08:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:33: 6000000 INFO @ Thu, 16 Apr 2020 05:08:33: 1000000 INFO @ Thu, 16 Apr 2020 05:08:40: 7000000 INFO @ Thu, 16 Apr 2020 05:08:41: 2000000 INFO @ Thu, 16 Apr 2020 05:08:47: 8000000 INFO @ Thu, 16 Apr 2020 05:08:49: 3000000 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 05:08:54: 9000000 INFO @ Thu, 16 Apr 2020 05:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.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 05:08:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:56: 4000000 INFO @ Thu, 16 Apr 2020 05:09:02: 10000000 INFO @ Thu, 16 Apr 2020 05:09:03: 1000000 INFO @ Thu, 16 Apr 2020 05:09:04: 5000000 INFO @ Thu, 16 Apr 2020 05:09:09: 11000000 INFO @ Thu, 16 Apr 2020 05:09:10: 2000000 INFO @ Thu, 16 Apr 2020 05:09:11: 6000000 INFO @ Thu, 16 Apr 2020 05:09:17: 12000000 INFO @ Thu, 16 Apr 2020 05:09:18: 3000000 INFO @ Thu, 16 Apr 2020 05:09:19: 7000000 INFO @ Thu, 16 Apr 2020 05:09:24: 13000000 INFO @ Thu, 16 Apr 2020 05:09:25: 4000000 INFO @ Thu, 16 Apr 2020 05:09:27: 8000000 INFO @ Thu, 16 Apr 2020 05:09:31: 14000000 INFO @ Thu, 16 Apr 2020 05:09:33: 5000000 INFO @ Thu, 16 Apr 2020 05:09:36: 9000000 INFO @ Thu, 16 Apr 2020 05:09:39: 15000000 INFO @ Thu, 16 Apr 2020 05:09:40: 6000000 INFO @ Thu, 16 Apr 2020 05:09:44: 10000000 INFO @ Thu, 16 Apr 2020 05:09:46: 16000000 INFO @ Thu, 16 Apr 2020 05:09:47: 7000000 INFO @ Thu, 16 Apr 2020 05:09:53: 11000000 INFO @ Thu, 16 Apr 2020 05:09:54: 17000000 INFO @ Thu, 16 Apr 2020 05:09:55: 8000000 INFO @ Thu, 16 Apr 2020 05:10:01: 12000000 INFO @ Thu, 16 Apr 2020 05:10:01: 18000000 INFO @ Thu, 16 Apr 2020 05:10:02: 9000000 INFO @ Thu, 16 Apr 2020 05:10:06: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:06: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:06: #1 total tags in treatment: 8767186 INFO @ Thu, 16 Apr 2020 05:10:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:06: #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 05:10:06: #1 tags after filtering in treatment: 8259625 INFO @ Thu, 16 Apr 2020 05:10:06: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:10:06: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:06: #2 number of paired peaks: 706 WARNING @ Thu, 16 Apr 2020 05:10:06: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:06: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:06: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:06: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:06: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:06: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:10:06: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05_model.r INFO @ Thu, 16 Apr 2020 05:10:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:09: 13000000 INFO @ Thu, 16 Apr 2020 05:10:10: 10000000 INFO @ Thu, 16 Apr 2020 05:10:17: 11000000 INFO @ Thu, 16 Apr 2020 05:10:17: 14000000 INFO @ Thu, 16 Apr 2020 05:10:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:24: 12000000 INFO @ Thu, 16 Apr 2020 05:10:25: 15000000 INFO @ Thu, 16 Apr 2020 05:10:32: 13000000 INFO @ Thu, 16 Apr 2020 05:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.05_summits.bed INFO @ Thu, 16 Apr 2020 05:10:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1921 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:10:33: 16000000 INFO @ Thu, 16 Apr 2020 05:10:39: 14000000 INFO @ Thu, 16 Apr 2020 05:10:40: 17000000 INFO @ Thu, 16 Apr 2020 05:10:46: 15000000 INFO @ Thu, 16 Apr 2020 05:10:48: 18000000 INFO @ Thu, 16 Apr 2020 05:10:52: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:52: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:52: #1 total tags in treatment: 8767186 INFO @ Thu, 16 Apr 2020 05:10:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:52: #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 05:10:52: #1 tags after filtering in treatment: 8259625 INFO @ Thu, 16 Apr 2020 05:10:52: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:10:52: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:53: #2 number of paired peaks: 706 WARNING @ Thu, 16 Apr 2020 05:10:53: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:53: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:53: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:53: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:53: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:53: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:10:53: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10_model.r INFO @ Thu, 16 Apr 2020 05:10:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:53: 16000000 INFO @ Thu, 16 Apr 2020 05:11:00: 17000000 INFO @ Thu, 16 Apr 2020 05:11:06: 18000000 INFO @ Thu, 16 Apr 2020 05:11:10: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:10: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:10: #1 total tags in treatment: 8767186 INFO @ Thu, 16 Apr 2020 05:11:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:10: #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 05:11:10: #1 tags after filtering in treatment: 8259625 INFO @ Thu, 16 Apr 2020 05:11:10: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:11:10: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:11: #2 number of paired peaks: 706 WARNING @ Thu, 16 Apr 2020 05:11:11: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Thu, 16 Apr 2020 05:11:11: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:11: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:11: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:11: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:11: #2 predicted fragment length is 171 bps INFO @ Thu, 16 Apr 2020 05:11:11: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 16 Apr 2020 05:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20_model.r INFO @ Thu, 16 Apr 2020 05:11:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.10_summits.bed INFO @ Thu, 16 Apr 2020 05:11:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:11:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708244/SRX6708244.20_summits.bed INFO @ Thu, 16 Apr 2020 05:11:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (572 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。