Job ID = 5721155 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,949,396 reads read : 27,898,792 reads written : 27,898,792 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: 00:21:08 13949396 reads; of these: 13949396 (100.00%) were paired; of these: 2829860 (20.29%) aligned concordantly 0 times 9064415 (64.98%) aligned concordantly exactly 1 time 2055121 (14.73%) aligned concordantly >1 times ---- 2829860 pairs aligned concordantly 0 times; of these: 252085 (8.91%) aligned discordantly 1 time ---- 2577775 pairs aligned 0 times concordantly or discordantly; of these: 5155550 mates make up the pairs; of these: 4601321 (89.25%) aligned 0 times 275381 (5.34%) aligned exactly 1 time 278848 (5.41%) aligned >1 times 83.51% overall alignment rate Time searching: 00:21:08 Overall time: 00:21:08 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] 602153 / 11363936 = 0.0530 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 05:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.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 05:57:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:57:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:57:34: 1000000 INFO @ Thu, 16 Apr 2020 05:57:39: 2000000 INFO @ Thu, 16 Apr 2020 05:57:44: 3000000 INFO @ Thu, 16 Apr 2020 05:57:49: 4000000 INFO @ Thu, 16 Apr 2020 05:57:54: 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 05:57:59: 6000000 INFO @ Thu, 16 Apr 2020 05:58:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.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 05:58:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:04: 7000000 INFO @ Thu, 16 Apr 2020 05:58:05: 1000000 INFO @ Thu, 16 Apr 2020 05:58:10: 8000000 INFO @ Thu, 16 Apr 2020 05:58:11: 2000000 INFO @ Thu, 16 Apr 2020 05:58:15: 9000000 INFO @ Thu, 16 Apr 2020 05:58:16: 3000000 INFO @ Thu, 16 Apr 2020 05:58:21: 10000000 INFO @ Thu, 16 Apr 2020 05:58:22: 4000000 INFO @ Thu, 16 Apr 2020 05:58:26: 11000000 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 05:58:27: 5000000 INFO @ Thu, 16 Apr 2020 05:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.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 05:58:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:32: 12000000 INFO @ Thu, 16 Apr 2020 05:58:33: 6000000 INFO @ Thu, 16 Apr 2020 05:58:35: 1000000 INFO @ Thu, 16 Apr 2020 05:58:37: 13000000 INFO @ Thu, 16 Apr 2020 05:58:38: 7000000 INFO @ Thu, 16 Apr 2020 05:58:41: 2000000 INFO @ Thu, 16 Apr 2020 05:58:43: 14000000 INFO @ Thu, 16 Apr 2020 05:58:44: 8000000 INFO @ Thu, 16 Apr 2020 05:58:46: 3000000 INFO @ Thu, 16 Apr 2020 05:58:48: 15000000 INFO @ Thu, 16 Apr 2020 05:58:49: 9000000 INFO @ Thu, 16 Apr 2020 05:58:52: 4000000 INFO @ Thu, 16 Apr 2020 05:58:54: 16000000 INFO @ Thu, 16 Apr 2020 05:58:55: 10000000 INFO @ Thu, 16 Apr 2020 05:58:57: 5000000 INFO @ Thu, 16 Apr 2020 05:58:59: 17000000 INFO @ Thu, 16 Apr 2020 05:59:00: 11000000 INFO @ Thu, 16 Apr 2020 05:59:03: 6000000 INFO @ Thu, 16 Apr 2020 05:59:05: 18000000 INFO @ Thu, 16 Apr 2020 05:59:06: 12000000 INFO @ Thu, 16 Apr 2020 05:59:08: 7000000 INFO @ Thu, 16 Apr 2020 05:59:10: 19000000 INFO @ Thu, 16 Apr 2020 05:59:11: 13000000 INFO @ Thu, 16 Apr 2020 05:59:14: 8000000 INFO @ Thu, 16 Apr 2020 05:59:16: 20000000 INFO @ Thu, 16 Apr 2020 05:59:17: 14000000 INFO @ Thu, 16 Apr 2020 05:59:20: 9000000 INFO @ Thu, 16 Apr 2020 05:59:21: 21000000 INFO @ Thu, 16 Apr 2020 05:59:22: 15000000 INFO @ Thu, 16 Apr 2020 05:59:25: 10000000 INFO @ Thu, 16 Apr 2020 05:59:27: 22000000 INFO @ Thu, 16 Apr 2020 05:59:27: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:59:27: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:59:27: #1 total tags in treatment: 10525074 INFO @ Thu, 16 Apr 2020 05:59:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:27: #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 05:59:27: #1 tags after filtering in treatment: 8825249 INFO @ Thu, 16 Apr 2020 05:59:27: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 05:59:27: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:28: 16000000 INFO @ Thu, 16 Apr 2020 05:59:28: #2 number of paired peaks: 4896 INFO @ Thu, 16 Apr 2020 05:59:28: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:28: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:28: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:28: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:28: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 05:59:28: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 05:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05_model.r INFO @ Thu, 16 Apr 2020 05:59:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:31: 11000000 INFO @ Thu, 16 Apr 2020 05:59:33: 17000000 INFO @ Thu, 16 Apr 2020 05:59:36: 12000000 INFO @ Thu, 16 Apr 2020 05:59:39: 18000000 INFO @ Thu, 16 Apr 2020 05:59:42: 13000000 INFO @ Thu, 16 Apr 2020 05:59:44: 19000000 INFO @ Thu, 16 Apr 2020 05:59:47: 14000000 INFO @ Thu, 16 Apr 2020 05:59:50: 20000000 INFO @ Thu, 16 Apr 2020 05:59:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:53: 15000000 INFO @ Thu, 16 Apr 2020 05:59:55: 21000000 INFO @ Thu, 16 Apr 2020 05:59:58: 16000000 INFO @ Thu, 16 Apr 2020 06:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:01: 22000000 INFO @ Thu, 16 Apr 2020 06:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.05_summits.bed INFO @ Thu, 16 Apr 2020 06:00:01: Done! INFO @ Thu, 16 Apr 2020 06:00:01: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:01: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:01: #1 total tags in treatment: 10525074 INFO @ Thu, 16 Apr 2020 06:00:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:01: #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 06:00:01: #1 tags after filtering in treatment: 8825249 INFO @ Thu, 16 Apr 2020 06:00:01: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:00:01: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:02: #2 number of paired peaks: 4896 INFO @ Thu, 16 Apr 2020 06:00:02: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:02: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:02: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:02: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:02: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 06:00:02: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 06:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10_model.r INFO @ Thu, 16 Apr 2020 06:00:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:03: 17000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8617 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:09: 18000000 INFO @ Thu, 16 Apr 2020 06:00:14: 19000000 INFO @ Thu, 16 Apr 2020 06:00:19: 20000000 INFO @ Thu, 16 Apr 2020 06:00:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:24: 21000000 INFO @ Thu, 16 Apr 2020 06:00:30: 22000000 INFO @ Thu, 16 Apr 2020 06:00:30: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:30: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:30: #1 total tags in treatment: 10525074 INFO @ Thu, 16 Apr 2020 06:00:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:30: #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 06:00:30: #1 tags after filtering in treatment: 8825249 INFO @ Thu, 16 Apr 2020 06:00:30: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:00:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:31: #2 number of paired peaks: 4896 INFO @ Thu, 16 Apr 2020 06:00:31: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:31: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:31: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:31: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:31: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 06:00:31: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 06:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20_model.r INFO @ Thu, 16 Apr 2020 06:00:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.10_summits.bed INFO @ Thu, 16 Apr 2020 06:00:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6920 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708293/SRX6708293.20_summits.bed INFO @ Thu, 16 Apr 2020 06:01:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5318 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。