Job ID = 5721106 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:42:01 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 : 11,355,887 reads read : 22,711,774 reads written : 22,711,774 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: 00:23:01 11355887 reads; of these: 11355887 (100.00%) were paired; of these: 1159787 (10.21%) aligned concordantly 0 times 7411725 (65.27%) aligned concordantly exactly 1 time 2784375 (24.52%) aligned concordantly >1 times ---- 1159787 pairs aligned concordantly 0 times; of these: 383566 (33.07%) aligned discordantly 1 time ---- 776221 pairs aligned 0 times concordantly or discordantly; of these: 1552442 mates make up the pairs; of these: 814472 (52.46%) aligned 0 times 389932 (25.12%) aligned exactly 1 time 348038 (22.42%) aligned >1 times 96.41% overall alignment rate Time searching: 00:23:01 Overall time: 00:23:01 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] 926593 / 10526686 = 0.0880 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 05:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.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 05:16:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:16:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:16:38: 1000000 INFO @ Thu, 16 Apr 2020 05:16:43: 2000000 INFO @ Thu, 16 Apr 2020 05:16:48: 3000000 INFO @ Thu, 16 Apr 2020 05:16:53: 4000000 INFO @ Thu, 16 Apr 2020 05:16:58: 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 05:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.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 05:17:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:17:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:17:04: 6000000 INFO @ Thu, 16 Apr 2020 05:17:09: 1000000 INFO @ Thu, 16 Apr 2020 05:17:09: 7000000 INFO @ Thu, 16 Apr 2020 05:17:14: 8000000 INFO @ Thu, 16 Apr 2020 05:17:14: 2000000 INFO @ Thu, 16 Apr 2020 05:17:19: 9000000 INFO @ Thu, 16 Apr 2020 05:17:19: 3000000 INFO @ Thu, 16 Apr 2020 05:17:24: 10000000 INFO @ Thu, 16 Apr 2020 05:17:24: 4000000 INFO @ Thu, 16 Apr 2020 05:17:29: 11000000 INFO @ Thu, 16 Apr 2020 05:17:30: 5000000 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 05:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.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 05:17:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:17:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:17:34: 12000000 INFO @ Thu, 16 Apr 2020 05:17:36: 6000000 INFO @ Thu, 16 Apr 2020 05:17:39: 1000000 INFO @ Thu, 16 Apr 2020 05:17:39: 13000000 INFO @ Thu, 16 Apr 2020 05:17:41: 7000000 INFO @ Thu, 16 Apr 2020 05:17:44: 14000000 INFO @ Thu, 16 Apr 2020 05:17:44: 2000000 INFO @ Thu, 16 Apr 2020 05:17:47: 8000000 INFO @ Thu, 16 Apr 2020 05:17:49: 15000000 INFO @ Thu, 16 Apr 2020 05:17:49: 3000000 INFO @ Thu, 16 Apr 2020 05:17:52: 9000000 INFO @ Thu, 16 Apr 2020 05:17:54: 16000000 INFO @ Thu, 16 Apr 2020 05:17:54: 4000000 INFO @ Thu, 16 Apr 2020 05:17:57: 10000000 INFO @ Thu, 16 Apr 2020 05:17:59: 17000000 INFO @ Thu, 16 Apr 2020 05:17:59: 5000000 INFO @ Thu, 16 Apr 2020 05:18:02: 11000000 INFO @ Thu, 16 Apr 2020 05:18:04: 18000000 INFO @ Thu, 16 Apr 2020 05:18:05: 6000000 INFO @ Thu, 16 Apr 2020 05:18:07: 12000000 INFO @ Thu, 16 Apr 2020 05:18:09: 19000000 INFO @ Thu, 16 Apr 2020 05:18:11: 7000000 INFO @ Thu, 16 Apr 2020 05:18:12: 13000000 INFO @ Thu, 16 Apr 2020 05:18:14: 20000000 INFO @ Thu, 16 Apr 2020 05:18:14: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:18:14: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:18:14: #1 total tags in treatment: 9287610 INFO @ Thu, 16 Apr 2020 05:18:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:18:14: #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 05:18:14: #1 tags after filtering in treatment: 8719285 INFO @ Thu, 16 Apr 2020 05:18:14: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:18:14: #1 finished! INFO @ Thu, 16 Apr 2020 05:18:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:18:15: #2 number of paired peaks: 907 WARNING @ Thu, 16 Apr 2020 05:18:15: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 16 Apr 2020 05:18:15: start model_add_line... INFO @ Thu, 16 Apr 2020 05:18:15: start X-correlation... INFO @ Thu, 16 Apr 2020 05:18:15: end of X-cor INFO @ Thu, 16 Apr 2020 05:18:15: #2 finished! INFO @ Thu, 16 Apr 2020 05:18:15: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 05:18:15: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 05:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05_model.r INFO @ Thu, 16 Apr 2020 05:18:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:18:16: 8000000 INFO @ Thu, 16 Apr 2020 05:18:17: 14000000 INFO @ Thu, 16 Apr 2020 05:18:21: 9000000 INFO @ Thu, 16 Apr 2020 05:18:22: 15000000 INFO @ Thu, 16 Apr 2020 05:18:26: 10000000 INFO @ Thu, 16 Apr 2020 05:18:26: 16000000 INFO @ Thu, 16 Apr 2020 05:18:31: 11000000 INFO @ Thu, 16 Apr 2020 05:18:31: 17000000 INFO @ Thu, 16 Apr 2020 05:18:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:18:36: 12000000 INFO @ Thu, 16 Apr 2020 05:18:36: 18000000 INFO @ Thu, 16 Apr 2020 05:18:41: 13000000 INFO @ Thu, 16 Apr 2020 05:18:41: 19000000 INFO @ Thu, 16 Apr 2020 05:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.05_summits.bed INFO @ Thu, 16 Apr 2020 05:18:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:18:46: 14000000 INFO @ Thu, 16 Apr 2020 05:18:46: 20000000 INFO @ Thu, 16 Apr 2020 05:18:47: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:18:47: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:18:47: #1 total tags in treatment: 9287610 INFO @ Thu, 16 Apr 2020 05:18:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:18:47: #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 05:18:47: #1 tags after filtering in treatment: 8719285 INFO @ Thu, 16 Apr 2020 05:18:47: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:18:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:18:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:18:47: #2 number of paired peaks: 907 WARNING @ Thu, 16 Apr 2020 05:18:47: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 16 Apr 2020 05:18:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:18:48: start X-correlation... INFO @ Thu, 16 Apr 2020 05:18:48: end of X-cor INFO @ Thu, 16 Apr 2020 05:18:48: #2 finished! INFO @ Thu, 16 Apr 2020 05:18:48: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 05:18:48: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 05:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10_model.r INFO @ Thu, 16 Apr 2020 05:18:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:18:50: 15000000 INFO @ Thu, 16 Apr 2020 05:18:55: 16000000 INFO @ Thu, 16 Apr 2020 05:19:00: 17000000 INFO @ Thu, 16 Apr 2020 05:19:05: 18000000 INFO @ Thu, 16 Apr 2020 05:19:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:19:10: 19000000 INFO @ Thu, 16 Apr 2020 05:19:15: 20000000 INFO @ Thu, 16 Apr 2020 05:19:15: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:19:15: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:19:15: #1 total tags in treatment: 9287610 INFO @ Thu, 16 Apr 2020 05:19:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:19:15: #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 05:19:15: #1 tags after filtering in treatment: 8719285 INFO @ Thu, 16 Apr 2020 05:19:15: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:19:15: #1 finished! INFO @ Thu, 16 Apr 2020 05:19:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:19:16: #2 number of paired peaks: 907 WARNING @ Thu, 16 Apr 2020 05:19:16: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Thu, 16 Apr 2020 05:19:16: start model_add_line... INFO @ Thu, 16 Apr 2020 05:19:16: start X-correlation... INFO @ Thu, 16 Apr 2020 05:19:16: end of X-cor INFO @ Thu, 16 Apr 2020 05:19:16: #2 finished! INFO @ Thu, 16 Apr 2020 05:19:16: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 05:19:16: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 05:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20_model.r INFO @ Thu, 16 Apr 2020 05:19:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.10_summits.bed INFO @ Thu, 16 Apr 2020 05:19:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:19:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708250/SRX6708250.20_summits.bed INFO @ Thu, 16 Apr 2020 05:19:46: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (556 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。