Job ID = 5721110 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:41:22 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 ) 2020-04-15T19:41:23 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 : 7,228,697 reads read : 14,457,394 reads written : 14,457,394 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: 00:11:55 7228697 reads; of these: 7228697 (100.00%) were paired; of these: 822167 (11.37%) aligned concordantly 0 times 5152661 (71.28%) aligned concordantly exactly 1 time 1253869 (17.35%) aligned concordantly >1 times ---- 822167 pairs aligned concordantly 0 times; of these: 230758 (28.07%) aligned discordantly 1 time ---- 591409 pairs aligned 0 times concordantly or discordantly; of these: 1182818 mates make up the pairs; of these: 798997 (67.55%) aligned 0 times 199082 (16.83%) aligned exactly 1 time 184739 (15.62%) aligned >1 times 94.47% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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] 420143 / 6618180 = 0.0635 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 05:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.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 05:03:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:03:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:03:51: 1000000 INFO @ Thu, 16 Apr 2020 05:03:57: 2000000 INFO @ Thu, 16 Apr 2020 05:04:04: 3000000 INFO @ Thu, 16 Apr 2020 05:04:10: 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 05:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.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 05:04:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:04:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:04:16: 5000000 INFO @ Thu, 16 Apr 2020 05:04:23: 1000000 INFO @ Thu, 16 Apr 2020 05:04:23: 6000000 INFO @ Thu, 16 Apr 2020 05:04:29: 2000000 INFO @ Thu, 16 Apr 2020 05:04:29: 7000000 INFO @ Thu, 16 Apr 2020 05:04:36: 3000000 INFO @ Thu, 16 Apr 2020 05:04:36: 8000000 INFO @ Thu, 16 Apr 2020 05:04:42: 4000000 INFO @ Thu, 16 Apr 2020 05:04:42: 9000000 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 05:04:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.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 05:04:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:04:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:04:48: 5000000 INFO @ Thu, 16 Apr 2020 05:04:48: 10000000 INFO @ Thu, 16 Apr 2020 05:04:52: 1000000 INFO @ Thu, 16 Apr 2020 05:04:54: 6000000 INFO @ Thu, 16 Apr 2020 05:04:55: 11000000 INFO @ Thu, 16 Apr 2020 05:04:58: 2000000 INFO @ Thu, 16 Apr 2020 05:05:01: 7000000 INFO @ Thu, 16 Apr 2020 05:05:01: 12000000 INFO @ Thu, 16 Apr 2020 05:05:05: 3000000 INFO @ Thu, 16 Apr 2020 05:05:06: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:05:06: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:05:06: #1 total tags in treatment: 5998036 INFO @ Thu, 16 Apr 2020 05:05:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:05:06: #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 05:05:06: #1 tags after filtering in treatment: 5719621 INFO @ Thu, 16 Apr 2020 05:05:06: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:05:06: #1 finished! INFO @ Thu, 16 Apr 2020 05:05:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:05:07: #2 number of paired peaks: 445 WARNING @ Thu, 16 Apr 2020 05:05:07: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 16 Apr 2020 05:05:07: start model_add_line... INFO @ Thu, 16 Apr 2020 05:05:07: start X-correlation... INFO @ Thu, 16 Apr 2020 05:05:07: end of X-cor INFO @ Thu, 16 Apr 2020 05:05:07: #2 finished! INFO @ Thu, 16 Apr 2020 05:05:07: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:05:07: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05_model.r INFO @ Thu, 16 Apr 2020 05:05:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:05:07: 8000000 INFO @ Thu, 16 Apr 2020 05:05:11: 4000000 INFO @ Thu, 16 Apr 2020 05:05:13: 9000000 INFO @ Thu, 16 Apr 2020 05:05:18: 5000000 INFO @ Thu, 16 Apr 2020 05:05:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:05:20: 10000000 INFO @ Thu, 16 Apr 2020 05:05:24: 6000000 INFO @ Thu, 16 Apr 2020 05:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.05_summits.bed INFO @ Thu, 16 Apr 2020 05:05:25: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:05:26: 11000000 INFO @ Thu, 16 Apr 2020 05:05:30: 7000000 INFO @ Thu, 16 Apr 2020 05:05:32: 12000000 INFO @ Thu, 16 Apr 2020 05:05:36: 8000000 INFO @ Thu, 16 Apr 2020 05:05:37: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:05:37: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:05:37: #1 total tags in treatment: 5998036 INFO @ Thu, 16 Apr 2020 05:05:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:05:37: #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 05:05:37: #1 tags after filtering in treatment: 5719621 INFO @ Thu, 16 Apr 2020 05:05:37: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:05:37: #1 finished! INFO @ Thu, 16 Apr 2020 05:05:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:05:38: #2 number of paired peaks: 445 WARNING @ Thu, 16 Apr 2020 05:05:38: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 16 Apr 2020 05:05:38: start model_add_line... INFO @ Thu, 16 Apr 2020 05:05:38: start X-correlation... INFO @ Thu, 16 Apr 2020 05:05:38: end of X-cor INFO @ Thu, 16 Apr 2020 05:05:38: #2 finished! INFO @ Thu, 16 Apr 2020 05:05:38: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:05:38: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:05:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10_model.r INFO @ Thu, 16 Apr 2020 05:05:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:05:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:05:42: 9000000 INFO @ Thu, 16 Apr 2020 05:05:48: 10000000 INFO @ Thu, 16 Apr 2020 05:05:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:05:54: 11000000 INFO @ Thu, 16 Apr 2020 05:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.10_summits.bed INFO @ Thu, 16 Apr 2020 05:05:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:06:00: 12000000 INFO @ Thu, 16 Apr 2020 05:06:05: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:06:05: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:06:05: #1 total tags in treatment: 5998036 INFO @ Thu, 16 Apr 2020 05:06:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:06:05: #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 05:06:05: #1 tags after filtering in treatment: 5719621 INFO @ Thu, 16 Apr 2020 05:06:05: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:06:05: #1 finished! INFO @ Thu, 16 Apr 2020 05:06:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:06:05: #2 number of paired peaks: 445 WARNING @ Thu, 16 Apr 2020 05:06:05: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Thu, 16 Apr 2020 05:06:05: start model_add_line... INFO @ Thu, 16 Apr 2020 05:06:05: start X-correlation... INFO @ Thu, 16 Apr 2020 05:06:05: end of X-cor INFO @ Thu, 16 Apr 2020 05:06:05: #2 finished! INFO @ Thu, 16 Apr 2020 05:06:05: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 05:06:05: #2 alternative fragment length(s) may be 189 bps INFO @ Thu, 16 Apr 2020 05:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20_model.r INFO @ Thu, 16 Apr 2020 05:06:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:06:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708254/SRX6708254.20_summits.bed INFO @ Thu, 16 Apr 2020 05:06:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (279 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。