Job ID = 5721150 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:28:09 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,053,276 reads read : 28,106,552 reads written : 28,106,552 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: 00:20:10 14053276 reads; of these: 14053276 (100.00%) were paired; of these: 2816373 (20.04%) aligned concordantly 0 times 9273639 (65.99%) aligned concordantly exactly 1 time 1963264 (13.97%) aligned concordantly >1 times ---- 2816373 pairs aligned concordantly 0 times; of these: 241416 (8.57%) aligned discordantly 1 time ---- 2574957 pairs aligned 0 times concordantly or discordantly; of these: 5149914 mates make up the pairs; of these: 4622126 (89.75%) aligned 0 times 266559 (5.18%) aligned exactly 1 time 261229 (5.07%) aligned >1 times 83.55% overall alignment rate Time searching: 00:20:10 Overall time: 00:20:10 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] 538213 / 11471594 = 0.0469 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 05:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.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 05:57:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:57:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:57:59: 1000000 INFO @ Thu, 16 Apr 2020 05:58:03: 2000000 INFO @ Thu, 16 Apr 2020 05:58:08: 3000000 INFO @ Thu, 16 Apr 2020 05:58:13: 4000000 INFO @ Thu, 16 Apr 2020 05:58:17: 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 05:58:22: 6000000 INFO @ Thu, 16 Apr 2020 05:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.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 05:58:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:27: 7000000 INFO @ Thu, 16 Apr 2020 05:58:30: 1000000 INFO @ Thu, 16 Apr 2020 05:58:32: 8000000 INFO @ Thu, 16 Apr 2020 05:58:34: 2000000 INFO @ Thu, 16 Apr 2020 05:58:36: 9000000 INFO @ Thu, 16 Apr 2020 05:58:39: 3000000 INFO @ Thu, 16 Apr 2020 05:58:41: 10000000 INFO @ Thu, 16 Apr 2020 05:58:44: 4000000 INFO @ Thu, 16 Apr 2020 05:58:46: 11000000 INFO @ Thu, 16 Apr 2020 05:58:49: 5000000 INFO @ Thu, 16 Apr 2020 05:58:51: 12000000 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 05:58:54: 6000000 INFO @ Thu, 16 Apr 2020 05:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.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 05:58:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:56: 13000000 INFO @ Thu, 16 Apr 2020 05:58:58: 7000000 INFO @ Thu, 16 Apr 2020 05:59:00: 14000000 INFO @ Thu, 16 Apr 2020 05:59:02: 1000000 INFO @ Thu, 16 Apr 2020 05:59:03: 8000000 INFO @ Thu, 16 Apr 2020 05:59:05: 15000000 INFO @ Thu, 16 Apr 2020 05:59:08: 2000000 INFO @ Thu, 16 Apr 2020 05:59:08: 9000000 INFO @ Thu, 16 Apr 2020 05:59:10: 16000000 INFO @ Thu, 16 Apr 2020 05:59:13: 3000000 INFO @ Thu, 16 Apr 2020 05:59:13: 10000000 INFO @ Thu, 16 Apr 2020 05:59:15: 17000000 INFO @ Thu, 16 Apr 2020 05:59:17: 4000000 INFO @ Thu, 16 Apr 2020 05:59:18: 11000000 INFO @ Thu, 16 Apr 2020 05:59:20: 18000000 INFO @ Thu, 16 Apr 2020 05:59:22: 5000000 INFO @ Thu, 16 Apr 2020 05:59:22: 12000000 INFO @ Thu, 16 Apr 2020 05:59:24: 19000000 INFO @ Thu, 16 Apr 2020 05:59:27: 6000000 INFO @ Thu, 16 Apr 2020 05:59:27: 13000000 INFO @ Thu, 16 Apr 2020 05:59:29: 20000000 INFO @ Thu, 16 Apr 2020 05:59:32: 7000000 INFO @ Thu, 16 Apr 2020 05:59:32: 14000000 INFO @ Thu, 16 Apr 2020 05:59:34: 21000000 INFO @ Thu, 16 Apr 2020 05:59:36: 8000000 INFO @ Thu, 16 Apr 2020 05:59:37: 15000000 INFO @ Thu, 16 Apr 2020 05:59:39: 22000000 INFO @ Thu, 16 Apr 2020 05:59:41: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:59:41: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:59:41: #1 total tags in treatment: 10705318 INFO @ Thu, 16 Apr 2020 05:59:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:41: #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 05:59:41: #1 tags after filtering in treatment: 9152296 INFO @ Thu, 16 Apr 2020 05:59:41: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:59:41: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:41: 9000000 INFO @ Thu, 16 Apr 2020 05:59:42: 16000000 INFO @ Thu, 16 Apr 2020 05:59:42: #2 number of paired peaks: 5183 INFO @ Thu, 16 Apr 2020 05:59:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:42: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:59:42: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05_model.r INFO @ Thu, 16 Apr 2020 05:59:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:46: 10000000 INFO @ Thu, 16 Apr 2020 05:59:46: 17000000 INFO @ Thu, 16 Apr 2020 05:59:51: 11000000 INFO @ Thu, 16 Apr 2020 05:59:51: 18000000 INFO @ Thu, 16 Apr 2020 05:59:56: 12000000 INFO @ Thu, 16 Apr 2020 05:59:56: 19000000 INFO @ Thu, 16 Apr 2020 06:00:00: 13000000 INFO @ Thu, 16 Apr 2020 06:00:01: 20000000 INFO @ Thu, 16 Apr 2020 06:00:05: 14000000 INFO @ Thu, 16 Apr 2020 06:00:05: 21000000 INFO @ Thu, 16 Apr 2020 06:00:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:10: 15000000 INFO @ Thu, 16 Apr 2020 06:00:10: 22000000 INFO @ Thu, 16 Apr 2020 06:00:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:12: #1 total tags in treatment: 10705318 INFO @ Thu, 16 Apr 2020 06:00:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:12: #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 06:00:12: #1 tags after filtering in treatment: 9152296 INFO @ Thu, 16 Apr 2020 06:00:12: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:00:12: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:13: #2 number of paired peaks: 5183 INFO @ Thu, 16 Apr 2020 06:00:13: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:13: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:13: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:13: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:13: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 06:00:13: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 06:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10_model.r INFO @ Thu, 16 Apr 2020 06:00:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:15: 16000000 INFO @ Thu, 16 Apr 2020 06:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.05_summits.bed INFO @ Thu, 16 Apr 2020 06:00:17: Done! INFO @ Thu, 16 Apr 2020 06:00:19: 17000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8706 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:24: 18000000 INFO @ Thu, 16 Apr 2020 06:00:29: 19000000 INFO @ Thu, 16 Apr 2020 06:00:33: 20000000 INFO @ Thu, 16 Apr 2020 06:00:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:38: 21000000 INFO @ Thu, 16 Apr 2020 06:00:42: 22000000 INFO @ Thu, 16 Apr 2020 06:00:44: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:00:44: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:00:44: #1 total tags in treatment: 10705318 INFO @ Thu, 16 Apr 2020 06:00:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:44: #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 06:00:44: #1 tags after filtering in treatment: 9152296 INFO @ Thu, 16 Apr 2020 06:00:44: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 06:00:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:45: #2 number of paired peaks: 5183 INFO @ Thu, 16 Apr 2020 06:00:45: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:45: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:45: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:45: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:45: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 06:00:45: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 06:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20_model.r INFO @ Thu, 16 Apr 2020 06:00:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.10_summits.bed INFO @ Thu, 16 Apr 2020 06:00:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6882 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:01:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708288/SRX6708288.20_summits.bed INFO @ Thu, 16 Apr 2020 06:01:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4946 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。