Job ID = 5720807 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:36:45 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 ) 2020-04-15T16:36:45 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 ) 2020-04-15T16:43:17 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 : 14,509,923 reads read : 29,019,846 reads written : 29,019,846 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: 00:18:16 14509923 reads; of these: 14509923 (100.00%) were paired; of these: 6005644 (41.39%) aligned concordantly 0 times 6886374 (47.46%) aligned concordantly exactly 1 time 1617905 (11.15%) aligned concordantly >1 times ---- 6005644 pairs aligned concordantly 0 times; of these: 49405 (0.82%) aligned discordantly 1 time ---- 5956239 pairs aligned 0 times concordantly or discordantly; of these: 11912478 mates make up the pairs; of these: 11295375 (94.82%) aligned 0 times 287178 (2.41%) aligned exactly 1 time 329925 (2.77%) aligned >1 times 61.08% overall alignment rate Time searching: 00:18:16 Overall time: 00:18:16 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 8 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] 3158458 / 8510763 = 0.3711 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 02:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.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 02:08:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:08:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:08:55: 1000000 INFO @ Thu, 16 Apr 2020 02:09:01: 2000000 INFO @ Thu, 16 Apr 2020 02:09:07: 3000000 INFO @ Thu, 16 Apr 2020 02:09:14: 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 02:09:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.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 02:09:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:09:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:09:20: 5000000 INFO @ Thu, 16 Apr 2020 02:09:24: 1000000 INFO @ Thu, 16 Apr 2020 02:09:27: 6000000 INFO @ Thu, 16 Apr 2020 02:09:31: 2000000 INFO @ Thu, 16 Apr 2020 02:09:33: 7000000 INFO @ Thu, 16 Apr 2020 02:09:38: 3000000 INFO @ Thu, 16 Apr 2020 02:09:40: 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 02:09:45: 4000000 INFO @ Thu, 16 Apr 2020 02:09:46: 9000000 INFO @ Thu, 16 Apr 2020 02:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.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 02:09:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:09:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:09:52: 5000000 INFO @ Thu, 16 Apr 2020 02:09:53: 10000000 INFO @ Thu, 16 Apr 2020 02:09:55: 1000000 INFO @ Thu, 16 Apr 2020 02:09:59: 6000000 INFO @ Thu, 16 Apr 2020 02:10:00: 11000000 INFO @ Thu, 16 Apr 2020 02:10:01: 2000000 INFO @ Thu, 16 Apr 2020 02:10:02: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:10:02: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:10:02: #1 total tags in treatment: 5350939 INFO @ Thu, 16 Apr 2020 02:10:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:10:02: #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 02:10:02: #1 tags after filtering in treatment: 5228805 INFO @ Thu, 16 Apr 2020 02:10:02: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:10:02: #1 finished! INFO @ Thu, 16 Apr 2020 02:10:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:10:03: #2 number of paired peaks: 274 WARNING @ Thu, 16 Apr 2020 02:10:03: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Thu, 16 Apr 2020 02:10:03: start model_add_line... INFO @ Thu, 16 Apr 2020 02:10:03: start X-correlation... INFO @ Thu, 16 Apr 2020 02:10:03: end of X-cor INFO @ Thu, 16 Apr 2020 02:10:03: #2 finished! INFO @ Thu, 16 Apr 2020 02:10:03: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 02:10:03: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 02:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05_model.r INFO @ Thu, 16 Apr 2020 02:10:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:10:06: 7000000 INFO @ Thu, 16 Apr 2020 02:10:08: 3000000 INFO @ Thu, 16 Apr 2020 02:10:13: 8000000 INFO @ Thu, 16 Apr 2020 02:10:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:10:15: 4000000 INFO @ Thu, 16 Apr 2020 02:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.05_summits.bed INFO @ Thu, 16 Apr 2020 02:10:19: Done! INFO @ Thu, 16 Apr 2020 02:10:20: 9000000 INFO @ Thu, 16 Apr 2020 02:10:21: 5000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (783 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:10:27: 10000000 INFO @ Thu, 16 Apr 2020 02:10:28: 6000000 INFO @ Thu, 16 Apr 2020 02:10:34: 11000000 INFO @ Thu, 16 Apr 2020 02:10:34: 7000000 INFO @ Thu, 16 Apr 2020 02:10:37: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:10:37: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:10:37: #1 total tags in treatment: 5350939 INFO @ Thu, 16 Apr 2020 02:10:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:10:37: #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 02:10:37: #1 tags after filtering in treatment: 5228805 INFO @ Thu, 16 Apr 2020 02:10:37: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:10:37: #1 finished! INFO @ Thu, 16 Apr 2020 02:10:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:10:37: #2 number of paired peaks: 274 WARNING @ Thu, 16 Apr 2020 02:10:37: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Thu, 16 Apr 2020 02:10:37: start model_add_line... INFO @ Thu, 16 Apr 2020 02:10:38: start X-correlation... INFO @ Thu, 16 Apr 2020 02:10:38: end of X-cor INFO @ Thu, 16 Apr 2020 02:10:38: #2 finished! INFO @ Thu, 16 Apr 2020 02:10:38: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 02:10:38: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 02:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10_model.r INFO @ Thu, 16 Apr 2020 02:10:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:10:41: 8000000 INFO @ Thu, 16 Apr 2020 02:10:47: 9000000 INFO @ Thu, 16 Apr 2020 02:10:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:10:53: 10000000 INFO @ Thu, 16 Apr 2020 02:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.10_summits.bed INFO @ Thu, 16 Apr 2020 02:10:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:10:59: 11000000 INFO @ Thu, 16 Apr 2020 02:11:02: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:11:02: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:11:02: #1 total tags in treatment: 5350939 INFO @ Thu, 16 Apr 2020 02:11:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:11:02: #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 02:11:02: #1 tags after filtering in treatment: 5228805 INFO @ Thu, 16 Apr 2020 02:11:02: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 02:11:02: #1 finished! INFO @ Thu, 16 Apr 2020 02:11:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:11:02: #2 number of paired peaks: 274 WARNING @ Thu, 16 Apr 2020 02:11:02: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Thu, 16 Apr 2020 02:11:02: start model_add_line... INFO @ Thu, 16 Apr 2020 02:11:02: start X-correlation... INFO @ Thu, 16 Apr 2020 02:11:02: end of X-cor INFO @ Thu, 16 Apr 2020 02:11:02: #2 finished! INFO @ Thu, 16 Apr 2020 02:11:02: #2 predicted fragment length is 186 bps INFO @ Thu, 16 Apr 2020 02:11:02: #2 alternative fragment length(s) may be 186 bps INFO @ Thu, 16 Apr 2020 02:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20_model.r INFO @ Thu, 16 Apr 2020 02:11:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:11:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309719/SRX5309719.20_summits.bed INFO @ Thu, 16 Apr 2020 02:11:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。