Job ID = 5720789 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,388,326 reads read : 42,776,652 reads written : 42,776,652 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: 02:02:03 21388326 reads; of these: 21388326 (100.00%) were paired; of these: 6024309 (28.17%) aligned concordantly 0 times 4959976 (23.19%) aligned concordantly exactly 1 time 10404041 (48.64%) aligned concordantly >1 times ---- 6024309 pairs aligned concordantly 0 times; of these: 719222 (11.94%) aligned discordantly 1 time ---- 5305087 pairs aligned 0 times concordantly or discordantly; of these: 10610174 mates make up the pairs; of these: 3621703 (34.13%) aligned 0 times 923033 (8.70%) aligned exactly 1 time 6065438 (57.17%) aligned >1 times 91.53% overall alignment rate Time searching: 02:02:03 Overall time: 02:02:03 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 20 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] 2140637 / 16005782 = 0.1337 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 04:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.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 04:06:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:06:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:06:30: 1000000 INFO @ Thu, 16 Apr 2020 04:06:37: 2000000 INFO @ Thu, 16 Apr 2020 04:06:43: 3000000 INFO @ Thu, 16 Apr 2020 04:06:50: 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 04:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.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 04:06:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:06:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:06:57: 5000000 INFO @ Thu, 16 Apr 2020 04:07:03: 1000000 INFO @ Thu, 16 Apr 2020 04:07:05: 6000000 INFO @ Thu, 16 Apr 2020 04:07:13: 2000000 INFO @ Thu, 16 Apr 2020 04:07:13: 7000000 INFO @ Thu, 16 Apr 2020 04:07:21: 8000000 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 04:07:22: 3000000 INFO @ Thu, 16 Apr 2020 04:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.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 04:07:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:07:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:07:29: 9000000 INFO @ Thu, 16 Apr 2020 04:07:32: 4000000 INFO @ Thu, 16 Apr 2020 04:07:32: 1000000 INFO @ Thu, 16 Apr 2020 04:07:38: 10000000 INFO @ Thu, 16 Apr 2020 04:07:41: 5000000 INFO @ Thu, 16 Apr 2020 04:07:41: 2000000 INFO @ Thu, 16 Apr 2020 04:07:46: 11000000 INFO @ Thu, 16 Apr 2020 04:07:50: 3000000 INFO @ Thu, 16 Apr 2020 04:07:50: 6000000 INFO @ Thu, 16 Apr 2020 04:07:55: 12000000 INFO @ Thu, 16 Apr 2020 04:07:58: 4000000 INFO @ Thu, 16 Apr 2020 04:08:00: 7000000 INFO @ Thu, 16 Apr 2020 04:08:03: 13000000 INFO @ Thu, 16 Apr 2020 04:08:07: 5000000 INFO @ Thu, 16 Apr 2020 04:08:09: 8000000 INFO @ Thu, 16 Apr 2020 04:08:12: 14000000 INFO @ Thu, 16 Apr 2020 04:08:15: 6000000 INFO @ Thu, 16 Apr 2020 04:08:18: 9000000 INFO @ Thu, 16 Apr 2020 04:08:20: 15000000 INFO @ Thu, 16 Apr 2020 04:08:24: 7000000 INFO @ Thu, 16 Apr 2020 04:08:27: 10000000 INFO @ Thu, 16 Apr 2020 04:08:28: 16000000 INFO @ Thu, 16 Apr 2020 04:08:32: 8000000 INFO @ Thu, 16 Apr 2020 04:08:36: 11000000 INFO @ Thu, 16 Apr 2020 04:08:37: 17000000 INFO @ Thu, 16 Apr 2020 04:08:41: 9000000 INFO @ Thu, 16 Apr 2020 04:08:46: 18000000 INFO @ Thu, 16 Apr 2020 04:08:46: 12000000 INFO @ Thu, 16 Apr 2020 04:08:50: 10000000 INFO @ Thu, 16 Apr 2020 04:08:55: 19000000 INFO @ Thu, 16 Apr 2020 04:08:56: 13000000 INFO @ Thu, 16 Apr 2020 04:08:58: 11000000 INFO @ Thu, 16 Apr 2020 04:09:03: 20000000 INFO @ Thu, 16 Apr 2020 04:09:05: 14000000 INFO @ Thu, 16 Apr 2020 04:09:07: 12000000 INFO @ Thu, 16 Apr 2020 04:09:12: 21000000 INFO @ Thu, 16 Apr 2020 04:09:15: 15000000 INFO @ Thu, 16 Apr 2020 04:09:15: 13000000 INFO @ Thu, 16 Apr 2020 04:09:20: 22000000 INFO @ Thu, 16 Apr 2020 04:09:24: 14000000 INFO @ Thu, 16 Apr 2020 04:09:25: 16000000 INFO @ Thu, 16 Apr 2020 04:09:29: 23000000 INFO @ Thu, 16 Apr 2020 04:09:32: 15000000 INFO @ Thu, 16 Apr 2020 04:09:35: 17000000 INFO @ Thu, 16 Apr 2020 04:09:38: 24000000 INFO @ Thu, 16 Apr 2020 04:09:41: 16000000 INFO @ Thu, 16 Apr 2020 04:09:45: 18000000 INFO @ Thu, 16 Apr 2020 04:09:46: 25000000 INFO @ Thu, 16 Apr 2020 04:09:50: 17000000 INFO @ Thu, 16 Apr 2020 04:09:54: 19000000 INFO @ Thu, 16 Apr 2020 04:09:54: 26000000 INFO @ Thu, 16 Apr 2020 04:09:59: 18000000 INFO @ Thu, 16 Apr 2020 04:10:03: 27000000 INFO @ Thu, 16 Apr 2020 04:10:04: 20000000 INFO @ Thu, 16 Apr 2020 04:10:07: 19000000 INFO @ Thu, 16 Apr 2020 04:10:11: 28000000 INFO @ Thu, 16 Apr 2020 04:10:13: 21000000 INFO @ Thu, 16 Apr 2020 04:10:16: 20000000 INFO @ Thu, 16 Apr 2020 04:10:20: 29000000 INFO @ Thu, 16 Apr 2020 04:10:22: 22000000 INFO @ Thu, 16 Apr 2020 04:10:24: 21000000 INFO @ Thu, 16 Apr 2020 04:10:28: 30000000 INFO @ Thu, 16 Apr 2020 04:10:31: 23000000 INFO @ Thu, 16 Apr 2020 04:10:33: 22000000 INFO @ Thu, 16 Apr 2020 04:10:37: 31000000 INFO @ Thu, 16 Apr 2020 04:10:41: 24000000 INFO @ Thu, 16 Apr 2020 04:10:42: 23000000 INFO @ Thu, 16 Apr 2020 04:10:46: 32000000 INFO @ Thu, 16 Apr 2020 04:10:50: 25000000 INFO @ Thu, 16 Apr 2020 04:10:51: 24000000 INFO @ Thu, 16 Apr 2020 04:10:54: 33000000 INFO @ Thu, 16 Apr 2020 04:10:59: 25000000 INFO @ Thu, 16 Apr 2020 04:10:59: 26000000 INFO @ Thu, 16 Apr 2020 04:11:03: 34000000 INFO @ Thu, 16 Apr 2020 04:11:08: 26000000 INFO @ Thu, 16 Apr 2020 04:11:09: 27000000 INFO @ Thu, 16 Apr 2020 04:11:11: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:11:11: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:11:11: #1 total tags in treatment: 13309512 INFO @ Thu, 16 Apr 2020 04:11:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:11:11: #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 04:11:11: #1 tags after filtering in treatment: 11329977 INFO @ Thu, 16 Apr 2020 04:11:11: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:11:11: #1 finished! INFO @ Thu, 16 Apr 2020 04:11:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:11:12: #2 number of paired peaks: 3813 INFO @ Thu, 16 Apr 2020 04:11:12: start model_add_line... INFO @ Thu, 16 Apr 2020 04:11:12: start X-correlation... INFO @ Thu, 16 Apr 2020 04:11:12: end of X-cor INFO @ Thu, 16 Apr 2020 04:11:12: #2 finished! INFO @ Thu, 16 Apr 2020 04:11:12: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:11:12: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05_model.r INFO @ Thu, 16 Apr 2020 04:11:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:11:17: 27000000 INFO @ Thu, 16 Apr 2020 04:11:18: 28000000 INFO @ Thu, 16 Apr 2020 04:11:25: 28000000 INFO @ Thu, 16 Apr 2020 04:11:27: 29000000 INFO @ Thu, 16 Apr 2020 04:11:34: 29000000 INFO @ Thu, 16 Apr 2020 04:11:36: 30000000 INFO @ Thu, 16 Apr 2020 04:11:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:11:42: 30000000 INFO @ Thu, 16 Apr 2020 04:11:45: 31000000 INFO @ Thu, 16 Apr 2020 04:11:51: 31000000 INFO @ Thu, 16 Apr 2020 04:11:54: 32000000 INFO @ Thu, 16 Apr 2020 04:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.05_summits.bed INFO @ Thu, 16 Apr 2020 04:11:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14305 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:12:00: 32000000 INFO @ Thu, 16 Apr 2020 04:12:04: 33000000 INFO @ Thu, 16 Apr 2020 04:12:09: 33000000 INFO @ Thu, 16 Apr 2020 04:12:13: 34000000 INFO @ Thu, 16 Apr 2020 04:12:17: 34000000 INFO @ Thu, 16 Apr 2020 04:12:21: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:12:21: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:12:21: #1 total tags in treatment: 13309512 INFO @ Thu, 16 Apr 2020 04:12:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:12:21: #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 04:12:21: #1 tags after filtering in treatment: 11329977 INFO @ Thu, 16 Apr 2020 04:12:21: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:12:21: #1 finished! INFO @ Thu, 16 Apr 2020 04:12:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:12:22: #2 number of paired peaks: 3813 INFO @ Thu, 16 Apr 2020 04:12:22: start model_add_line... INFO @ Thu, 16 Apr 2020 04:12:22: start X-correlation... INFO @ Thu, 16 Apr 2020 04:12:22: end of X-cor INFO @ Thu, 16 Apr 2020 04:12:22: #2 finished! INFO @ Thu, 16 Apr 2020 04:12:22: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:12:22: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10_model.r INFO @ Thu, 16 Apr 2020 04:12:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:12:25: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:12:25: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:12:25: #1 total tags in treatment: 13309512 INFO @ Thu, 16 Apr 2020 04:12:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:12:25: #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 04:12:25: #1 tags after filtering in treatment: 11329977 INFO @ Thu, 16 Apr 2020 04:12:25: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:12:25: #1 finished! INFO @ Thu, 16 Apr 2020 04:12:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:12:26: #2 number of paired peaks: 3813 INFO @ Thu, 16 Apr 2020 04:12:26: start model_add_line... INFO @ Thu, 16 Apr 2020 04:12:26: start X-correlation... INFO @ Thu, 16 Apr 2020 04:12:26: end of X-cor INFO @ Thu, 16 Apr 2020 04:12:26: #2 finished! INFO @ Thu, 16 Apr 2020 04:12:26: #2 predicted fragment length is 227 bps INFO @ Thu, 16 Apr 2020 04:12:26: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 16 Apr 2020 04:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20_model.r INFO @ Thu, 16 Apr 2020 04:12:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:12:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:12:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:12:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.10_summits.bed INFO @ Thu, 16 Apr 2020 04:13:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9612 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246881/SRX5246881.20_summits.bed INFO @ Thu, 16 Apr 2020 04:13:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5276 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。