Job ID = 5721116 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,305,338 reads read : 10,610,676 reads written : 10,610,676 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: 00:08:40 5305338 reads; of these: 5305338 (100.00%) were paired; of these: 952506 (17.95%) aligned concordantly 0 times 3505728 (66.08%) aligned concordantly exactly 1 time 847104 (15.97%) aligned concordantly >1 times ---- 952506 pairs aligned concordantly 0 times; of these: 365244 (38.35%) aligned discordantly 1 time ---- 587262 pairs aligned 0 times concordantly or discordantly; of these: 1174524 mates make up the pairs; of these: 661946 (56.36%) aligned 0 times 267557 (22.78%) aligned exactly 1 time 245021 (20.86%) aligned >1 times 93.76% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 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] 317469 / 4705827 = 0.0675 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 05:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.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 05:07:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:07:31: 1000000 INFO @ Thu, 16 Apr 2020 05:07:37: 2000000 INFO @ Thu, 16 Apr 2020 05:07:44: 3000000 INFO @ Thu, 16 Apr 2020 05:07:50: 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 05:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.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 05:07:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:07:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:07:56: 5000000 INFO @ Thu, 16 Apr 2020 05:08:01: 1000000 INFO @ Thu, 16 Apr 2020 05:08:03: 6000000 INFO @ Thu, 16 Apr 2020 05:08:07: 2000000 INFO @ Thu, 16 Apr 2020 05:08:10: 7000000 INFO @ Thu, 16 Apr 2020 05:08:13: 3000000 INFO @ Thu, 16 Apr 2020 05:08:16: 8000000 INFO @ Thu, 16 Apr 2020 05:08:19: 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 05:08:23: 9000000 INFO @ Thu, 16 Apr 2020 05:08:25: 5000000 INFO @ Thu, 16 Apr 2020 05:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.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 05:08:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:25: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:08:25: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:08:25: #1 total tags in treatment: 4056592 INFO @ Thu, 16 Apr 2020 05:08:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:08:25: #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 05:08:25: #1 tags after filtering in treatment: 3898110 INFO @ Thu, 16 Apr 2020 05:08:25: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:08:25: #1 finished! INFO @ Thu, 16 Apr 2020 05:08:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:08:25: #2 number of paired peaks: 1115 INFO @ Thu, 16 Apr 2020 05:08:25: start model_add_line... INFO @ Thu, 16 Apr 2020 05:08:26: start X-correlation... INFO @ Thu, 16 Apr 2020 05:08:26: end of X-cor INFO @ Thu, 16 Apr 2020 05:08:26: #2 finished! INFO @ Thu, 16 Apr 2020 05:08:26: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 05:08:26: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 05:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05_model.r INFO @ Thu, 16 Apr 2020 05:08:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:08:31: 6000000 INFO @ Thu, 16 Apr 2020 05:08:31: 1000000 INFO @ Thu, 16 Apr 2020 05:08:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:08:36: 7000000 INFO @ Thu, 16 Apr 2020 05:08:38: 2000000 INFO @ Thu, 16 Apr 2020 05:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.05_summits.bed INFO @ Thu, 16 Apr 2020 05:08:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2932 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:08:42: 8000000 INFO @ Thu, 16 Apr 2020 05:08:45: 3000000 INFO @ Thu, 16 Apr 2020 05:08:48: 9000000 INFO @ Thu, 16 Apr 2020 05:08:50: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:08:50: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:08:50: #1 total tags in treatment: 4056592 INFO @ Thu, 16 Apr 2020 05:08:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:08:50: #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 05:08:50: #1 tags after filtering in treatment: 3898110 INFO @ Thu, 16 Apr 2020 05:08:50: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:08:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:08:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:08:51: #2 number of paired peaks: 1115 INFO @ Thu, 16 Apr 2020 05:08:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:08:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:08:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:08:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:08:51: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 05:08:51: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 05:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10_model.r INFO @ Thu, 16 Apr 2020 05:08:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:08:51: 4000000 INFO @ Thu, 16 Apr 2020 05:08:58: 5000000 INFO @ Thu, 16 Apr 2020 05:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:09:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:09:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.10_summits.bed INFO @ Thu, 16 Apr 2020 05:09:04: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1042 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:09:04: 6000000 INFO @ Thu, 16 Apr 2020 05:09:11: 7000000 INFO @ Thu, 16 Apr 2020 05:09:18: 8000000 INFO @ Thu, 16 Apr 2020 05:09:24: 9000000 INFO @ Thu, 16 Apr 2020 05:09:26: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:09:26: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:09:26: #1 total tags in treatment: 4056592 INFO @ Thu, 16 Apr 2020 05:09:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:09:26: #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 05:09:26: #1 tags after filtering in treatment: 3898110 INFO @ Thu, 16 Apr 2020 05:09:26: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:09:26: #1 finished! INFO @ Thu, 16 Apr 2020 05:09:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:09:27: #2 number of paired peaks: 1115 INFO @ Thu, 16 Apr 2020 05:09:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:09:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:09:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:09:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:09:27: #2 predicted fragment length is 220 bps INFO @ Thu, 16 Apr 2020 05:09:27: #2 alternative fragment length(s) may be 220 bps INFO @ Thu, 16 Apr 2020 05:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20_model.r INFO @ Thu, 16 Apr 2020 05:09:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:09:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708259/SRX6708259.20_summits.bed INFO @ Thu, 16 Apr 2020 05:09:40: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (297 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。