Job ID = 5721143 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:19:18 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 : 21,054,621 reads read : 42,109,242 reads written : 42,109,242 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: 00:42:26 21054621 reads; of these: 21054621 (100.00%) were paired; of these: 5159040 (24.50%) aligned concordantly 0 times 10865889 (51.61%) aligned concordantly exactly 1 time 5029692 (23.89%) aligned concordantly >1 times ---- 5159040 pairs aligned concordantly 0 times; of these: 185946 (3.60%) aligned discordantly 1 time ---- 4973094 pairs aligned 0 times concordantly or discordantly; of these: 9946188 mates make up the pairs; of these: 9228656 (92.79%) aligned 0 times 396769 (3.99%) aligned exactly 1 time 320763 (3.22%) aligned >1 times 78.08% overall alignment rate Time searching: 00:42:26 Overall time: 00:42:26 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 16 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] 1089473 / 16038340 = 0.0679 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 06:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.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 06:23:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:27: 1000000 INFO @ Thu, 16 Apr 2020 06:23:32: 2000000 INFO @ Thu, 16 Apr 2020 06:23:37: 3000000 INFO @ Thu, 16 Apr 2020 06:23:41: 4000000 INFO @ Thu, 16 Apr 2020 06:23:46: 5000000 INFO @ Thu, 16 Apr 2020 06:23:50: 6000000 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 06:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.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 06:23:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:55: 7000000 INFO @ Thu, 16 Apr 2020 06:23:57: 1000000 INFO @ Thu, 16 Apr 2020 06:24:00: 8000000 INFO @ Thu, 16 Apr 2020 06:24:02: 2000000 INFO @ Thu, 16 Apr 2020 06:24:04: 9000000 INFO @ Thu, 16 Apr 2020 06:24:07: 3000000 INFO @ Thu, 16 Apr 2020 06:24:09: 10000000 INFO @ Thu, 16 Apr 2020 06:24:12: 4000000 INFO @ Thu, 16 Apr 2020 06:24:13: 11000000 INFO @ Thu, 16 Apr 2020 06:24:16: 5000000 INFO @ Thu, 16 Apr 2020 06:24:18: 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 06:24:21: 6000000 INFO @ Thu, 16 Apr 2020 06:24:22: 13000000 INFO @ Thu, 16 Apr 2020 06:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.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 06:24:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:26: 7000000 INFO @ Thu, 16 Apr 2020 06:24:27: 14000000 INFO @ Thu, 16 Apr 2020 06:24:28: 1000000 INFO @ Thu, 16 Apr 2020 06:24:30: 8000000 INFO @ Thu, 16 Apr 2020 06:24:32: 15000000 INFO @ Thu, 16 Apr 2020 06:24:34: 2000000 INFO @ Thu, 16 Apr 2020 06:24:35: 9000000 INFO @ Thu, 16 Apr 2020 06:24:36: 16000000 INFO @ Thu, 16 Apr 2020 06:24:39: 3000000 INFO @ Thu, 16 Apr 2020 06:24:40: 10000000 INFO @ Thu, 16 Apr 2020 06:24:41: 17000000 INFO @ Thu, 16 Apr 2020 06:24:44: 4000000 INFO @ Thu, 16 Apr 2020 06:24:44: 11000000 INFO @ Thu, 16 Apr 2020 06:24:46: 18000000 INFO @ Thu, 16 Apr 2020 06:24:49: 12000000 INFO @ Thu, 16 Apr 2020 06:24:49: 5000000 INFO @ Thu, 16 Apr 2020 06:24:50: 19000000 INFO @ Thu, 16 Apr 2020 06:24:53: 13000000 INFO @ Thu, 16 Apr 2020 06:24:55: 6000000 INFO @ Thu, 16 Apr 2020 06:24:55: 20000000 INFO @ Thu, 16 Apr 2020 06:24:58: 14000000 INFO @ Thu, 16 Apr 2020 06:25:00: 7000000 INFO @ Thu, 16 Apr 2020 06:25:00: 21000000 INFO @ Thu, 16 Apr 2020 06:25:03: 15000000 INFO @ Thu, 16 Apr 2020 06:25:04: 8000000 INFO @ Thu, 16 Apr 2020 06:25:04: 22000000 INFO @ Thu, 16 Apr 2020 06:25:07: 16000000 INFO @ Thu, 16 Apr 2020 06:25:09: 23000000 INFO @ Thu, 16 Apr 2020 06:25:09: 9000000 INFO @ Thu, 16 Apr 2020 06:25:12: 17000000 INFO @ Thu, 16 Apr 2020 06:25:14: 24000000 INFO @ Thu, 16 Apr 2020 06:25:14: 10000000 INFO @ Thu, 16 Apr 2020 06:25:17: 18000000 INFO @ Thu, 16 Apr 2020 06:25:18: 25000000 INFO @ Thu, 16 Apr 2020 06:25:19: 11000000 INFO @ Thu, 16 Apr 2020 06:25:22: 19000000 INFO @ Thu, 16 Apr 2020 06:25:23: 26000000 INFO @ Thu, 16 Apr 2020 06:25:24: 12000000 INFO @ Thu, 16 Apr 2020 06:25:26: 20000000 INFO @ Thu, 16 Apr 2020 06:25:28: 27000000 INFO @ Thu, 16 Apr 2020 06:25:29: 13000000 INFO @ Thu, 16 Apr 2020 06:25:31: 21000000 INFO @ Thu, 16 Apr 2020 06:25:32: 28000000 INFO @ Thu, 16 Apr 2020 06:25:34: 14000000 INFO @ Thu, 16 Apr 2020 06:25:36: 22000000 INFO @ Thu, 16 Apr 2020 06:25:37: 29000000 INFO @ Thu, 16 Apr 2020 06:25:39: 15000000 INFO @ Thu, 16 Apr 2020 06:25:40: 23000000 INFO @ Thu, 16 Apr 2020 06:25:42: 30000000 INFO @ Thu, 16 Apr 2020 06:25:44: 16000000 INFO @ Thu, 16 Apr 2020 06:25:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:25:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:25:45: #1 total tags in treatment: 14808770 INFO @ Thu, 16 Apr 2020 06:25:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:25:45: #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 06:25:45: 24000000 INFO @ Thu, 16 Apr 2020 06:25:45: #1 tags after filtering in treatment: 13910762 INFO @ Thu, 16 Apr 2020 06:25:45: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:25:45: #1 finished! INFO @ Thu, 16 Apr 2020 06:25:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:25:46: #2 number of paired peaks: 750 WARNING @ Thu, 16 Apr 2020 06:25:46: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 16 Apr 2020 06:25:46: start model_add_line... INFO @ Thu, 16 Apr 2020 06:25:46: start X-correlation... INFO @ Thu, 16 Apr 2020 06:25:46: end of X-cor INFO @ Thu, 16 Apr 2020 06:25:46: #2 finished! INFO @ Thu, 16 Apr 2020 06:25:46: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 06:25:46: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 06:25:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05_model.r INFO @ Thu, 16 Apr 2020 06:25:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:25:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:25:49: 17000000 INFO @ Thu, 16 Apr 2020 06:25:50: 25000000 INFO @ Thu, 16 Apr 2020 06:25:54: 18000000 INFO @ Thu, 16 Apr 2020 06:25:54: 26000000 INFO @ Thu, 16 Apr 2020 06:25:58: 19000000 INFO @ Thu, 16 Apr 2020 06:25:59: 27000000 INFO @ Thu, 16 Apr 2020 06:26:03: 20000000 INFO @ Thu, 16 Apr 2020 06:26:04: 28000000 INFO @ Thu, 16 Apr 2020 06:26:08: 21000000 INFO @ Thu, 16 Apr 2020 06:26:08: 29000000 INFO @ Thu, 16 Apr 2020 06:26:13: 22000000 INFO @ Thu, 16 Apr 2020 06:26:13: 30000000 INFO @ Thu, 16 Apr 2020 06:26:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:16: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:26:16: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:26:16: #1 total tags in treatment: 14808770 INFO @ Thu, 16 Apr 2020 06:26:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:16: #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 06:26:17: #1 tags after filtering in treatment: 13910762 INFO @ Thu, 16 Apr 2020 06:26:17: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:26:17: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:17: 23000000 INFO @ Thu, 16 Apr 2020 06:26:18: #2 number of paired peaks: 750 WARNING @ Thu, 16 Apr 2020 06:26:18: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:18: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 06:26:18: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 06:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10_model.r INFO @ Thu, 16 Apr 2020 06:26:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:22: 24000000 INFO @ Thu, 16 Apr 2020 06:26:27: 25000000 INFO @ Thu, 16 Apr 2020 06:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.05_summits.bed INFO @ Thu, 16 Apr 2020 06:26:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2483 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:26:32: 26000000 INFO @ Thu, 16 Apr 2020 06:26:36: 27000000 INFO @ Thu, 16 Apr 2020 06:26:41: 28000000 INFO @ Thu, 16 Apr 2020 06:26:46: 29000000 INFO @ Thu, 16 Apr 2020 06:26:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:50: 30000000 INFO @ Thu, 16 Apr 2020 06:26:54: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:26:54: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:26:54: #1 total tags in treatment: 14808770 INFO @ Thu, 16 Apr 2020 06:26:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:54: #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 06:26:54: #1 tags after filtering in treatment: 13910762 INFO @ Thu, 16 Apr 2020 06:26:54: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:26:54: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:55: #2 number of paired peaks: 750 WARNING @ Thu, 16 Apr 2020 06:26:55: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:55: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:55: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:55: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:55: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:55: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 06:26:55: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 06:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20_model.r INFO @ Thu, 16 Apr 2020 06:26:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.10_summits.bed INFO @ Thu, 16 Apr 2020 06:27:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:27:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708282/SRX6708282.20_summits.bed INFO @ Thu, 16 Apr 2020 06:27:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (844 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。