Job ID = 5721147 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,125,847 reads read : 28,251,694 reads written : 28,251,694 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: 00:30:51 14125847 reads; of these: 14125847 (100.00%) were paired; of these: 3219593 (22.79%) aligned concordantly 0 times 7325964 (51.86%) aligned concordantly exactly 1 time 3580290 (25.35%) aligned concordantly >1 times ---- 3219593 pairs aligned concordantly 0 times; of these: 115179 (3.58%) aligned discordantly 1 time ---- 3104414 pairs aligned 0 times concordantly or discordantly; of these: 6208828 mates make up the pairs; of these: 5697278 (91.76%) aligned 0 times 272892 (4.40%) aligned exactly 1 time 238658 (3.84%) aligned >1 times 79.83% overall alignment rate Time searching: 00:30:51 Overall time: 00:30:51 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] 881999 / 10985809 = 0.0803 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 06:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.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 06:03:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:03:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:03:22: 1000000 INFO @ Thu, 16 Apr 2020 06:03:28: 2000000 INFO @ Thu, 16 Apr 2020 06:03:33: 3000000 INFO @ Thu, 16 Apr 2020 06:03:38: 4000000 INFO @ Thu, 16 Apr 2020 06:03:44: 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 06:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.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 06:03:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:03:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:03:50: 6000000 INFO @ Thu, 16 Apr 2020 06:03:54: 1000000 INFO @ Thu, 16 Apr 2020 06:03:56: 7000000 INFO @ Thu, 16 Apr 2020 06:04:01: 2000000 INFO @ Thu, 16 Apr 2020 06:04:03: 8000000 INFO @ Thu, 16 Apr 2020 06:04:08: 3000000 INFO @ Thu, 16 Apr 2020 06:04:09: 9000000 INFO @ Thu, 16 Apr 2020 06:04:15: 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 06:04:15: 10000000 INFO @ Thu, 16 Apr 2020 06:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.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 06:04:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:04:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:04:22: 11000000 INFO @ Thu, 16 Apr 2020 06:04:22: 5000000 INFO @ Thu, 16 Apr 2020 06:04:25: 1000000 INFO @ Thu, 16 Apr 2020 06:04:28: 12000000 INFO @ Thu, 16 Apr 2020 06:04:30: 6000000 INFO @ Thu, 16 Apr 2020 06:04:32: 2000000 INFO @ Thu, 16 Apr 2020 06:04:35: 13000000 INFO @ Thu, 16 Apr 2020 06:04:37: 7000000 INFO @ Thu, 16 Apr 2020 06:04:39: 3000000 INFO @ Thu, 16 Apr 2020 06:04:41: 14000000 INFO @ Thu, 16 Apr 2020 06:04:44: 8000000 INFO @ Thu, 16 Apr 2020 06:04:47: 4000000 INFO @ Thu, 16 Apr 2020 06:04:48: 15000000 INFO @ Thu, 16 Apr 2020 06:04:52: 9000000 INFO @ Thu, 16 Apr 2020 06:04:54: 5000000 INFO @ Thu, 16 Apr 2020 06:04:54: 16000000 INFO @ Thu, 16 Apr 2020 06:04:59: 10000000 INFO @ Thu, 16 Apr 2020 06:05:01: 17000000 INFO @ Thu, 16 Apr 2020 06:05:01: 6000000 INFO @ Thu, 16 Apr 2020 06:05:06: 11000000 INFO @ Thu, 16 Apr 2020 06:05:07: 18000000 INFO @ Thu, 16 Apr 2020 06:05:09: 7000000 INFO @ Thu, 16 Apr 2020 06:05:13: 12000000 INFO @ Thu, 16 Apr 2020 06:05:14: 19000000 INFO @ Thu, 16 Apr 2020 06:05:16: 8000000 INFO @ Thu, 16 Apr 2020 06:05:20: 20000000 INFO @ Thu, 16 Apr 2020 06:05:21: 13000000 INFO @ Thu, 16 Apr 2020 06:05:23: 9000000 INFO @ Thu, 16 Apr 2020 06:05:25: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:05:25: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:05:25: #1 total tags in treatment: 10026399 INFO @ Thu, 16 Apr 2020 06:05:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:05:25: #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 06:05:26: #1 tags after filtering in treatment: 9512085 INFO @ Thu, 16 Apr 2020 06:05:26: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:05:26: #1 finished! INFO @ Thu, 16 Apr 2020 06:05:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:05:26: #2 number of paired peaks: 984 WARNING @ Thu, 16 Apr 2020 06:05:26: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Thu, 16 Apr 2020 06:05:26: start model_add_line... INFO @ Thu, 16 Apr 2020 06:05:26: start X-correlation... INFO @ Thu, 16 Apr 2020 06:05:26: end of X-cor INFO @ Thu, 16 Apr 2020 06:05:26: #2 finished! INFO @ Thu, 16 Apr 2020 06:05:26: #2 predicted fragment length is 173 bps INFO @ Thu, 16 Apr 2020 06:05:26: #2 alternative fragment length(s) may be 173 bps INFO @ Thu, 16 Apr 2020 06:05:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05_model.r INFO @ Thu, 16 Apr 2020 06:05:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:05:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:05:28: 14000000 INFO @ Thu, 16 Apr 2020 06:05:31: 10000000 INFO @ Thu, 16 Apr 2020 06:05:35: 15000000 INFO @ Thu, 16 Apr 2020 06:05:38: 11000000 INFO @ Thu, 16 Apr 2020 06:05:42: 16000000 INFO @ Thu, 16 Apr 2020 06:05:45: 12000000 INFO @ Thu, 16 Apr 2020 06:05:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:05:50: 17000000 INFO @ Thu, 16 Apr 2020 06:05:52: 13000000 INFO @ Thu, 16 Apr 2020 06:05:57: 18000000 INFO @ Thu, 16 Apr 2020 06:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.05_summits.bed INFO @ Thu, 16 Apr 2020 06:05:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2185 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:06:00: 14000000 INFO @ Thu, 16 Apr 2020 06:06:04: 19000000 INFO @ Thu, 16 Apr 2020 06:06:07: 15000000 INFO @ Thu, 16 Apr 2020 06:06:12: 20000000 INFO @ Thu, 16 Apr 2020 06:06:14: 16000000 INFO @ Thu, 16 Apr 2020 06:06:17: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:06:17: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:06:17: #1 total tags in treatment: 10026399 INFO @ Thu, 16 Apr 2020 06:06:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:06:17: #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 06:06:17: #1 tags after filtering in treatment: 9512085 INFO @ Thu, 16 Apr 2020 06:06:17: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:06:17: #1 finished! INFO @ Thu, 16 Apr 2020 06:06:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:06:18: #2 number of paired peaks: 984 WARNING @ Thu, 16 Apr 2020 06:06:18: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Thu, 16 Apr 2020 06:06:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:06:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:06:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:06:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:06:18: #2 predicted fragment length is 173 bps INFO @ Thu, 16 Apr 2020 06:06:18: #2 alternative fragment length(s) may be 173 bps INFO @ Thu, 16 Apr 2020 06:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10_model.r INFO @ Thu, 16 Apr 2020 06:06:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:06:21: 17000000 INFO @ Thu, 16 Apr 2020 06:06:28: 18000000 INFO @ Thu, 16 Apr 2020 06:06:35: 19000000 INFO @ Thu, 16 Apr 2020 06:06:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:06:41: 20000000 INFO @ Thu, 16 Apr 2020 06:06:47: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:06:47: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:06:47: #1 total tags in treatment: 10026399 INFO @ Thu, 16 Apr 2020 06:06:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:06:47: #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 06:06:47: #1 tags after filtering in treatment: 9512085 INFO @ Thu, 16 Apr 2020 06:06:47: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:06:47: #1 finished! INFO @ Thu, 16 Apr 2020 06:06:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:06:48: #2 number of paired peaks: 984 WARNING @ Thu, 16 Apr 2020 06:06:48: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Thu, 16 Apr 2020 06:06:48: start model_add_line... INFO @ Thu, 16 Apr 2020 06:06:48: start X-correlation... INFO @ Thu, 16 Apr 2020 06:06:48: end of X-cor INFO @ Thu, 16 Apr 2020 06:06:48: #2 finished! INFO @ Thu, 16 Apr 2020 06:06:48: #2 predicted fragment length is 173 bps INFO @ Thu, 16 Apr 2020 06:06:48: #2 alternative fragment length(s) may be 173 bps INFO @ Thu, 16 Apr 2020 06:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20_model.r INFO @ Thu, 16 Apr 2020 06:06:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:06:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.10_summits.bed INFO @ Thu, 16 Apr 2020 06:06:50: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1330 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:07:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708285/SRX6708285.20_summits.bed INFO @ Thu, 16 Apr 2020 06:07:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (704 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。