Job ID = 5721192 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:36:58 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 ) 2020-04-15T20:36:58 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 ) 2020-04-15T20:36:58 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 : 9,619,103 reads read : 9,619,103 reads written : 9,619,103 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: 00:02:47 9619103 reads; of these: 9619103 (100.00%) were unpaired; of these: 757614 (7.88%) aligned 0 times 6254693 (65.02%) aligned exactly 1 time 2606796 (27.10%) aligned >1 times 92.12% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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_rmdupse_core] 4403566 / 8861489 = 0.4969 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 05:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.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 05:47:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:47:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:47:11: 1000000 INFO @ Thu, 16 Apr 2020 05:47:17: 2000000 INFO @ Thu, 16 Apr 2020 05:47:22: 3000000 INFO @ Thu, 16 Apr 2020 05:47:28: 4000000 INFO @ Thu, 16 Apr 2020 05:47:30: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 05:47:30: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 05:47:30: #1 total tags in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:47:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:47:30: #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 05:47:30: #1 tags after filtering in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:47:30: #1 finished! INFO @ Thu, 16 Apr 2020 05:47:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:47:31: #2 number of paired peaks: 515 WARNING @ Thu, 16 Apr 2020 05:47:31: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Thu, 16 Apr 2020 05:47:31: start model_add_line... INFO @ Thu, 16 Apr 2020 05:47:31: start X-correlation... INFO @ Thu, 16 Apr 2020 05:47:31: end of X-cor INFO @ Thu, 16 Apr 2020 05:47:31: #2 finished! INFO @ Thu, 16 Apr 2020 05:47:31: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 05:47:31: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 05:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05_model.r INFO @ Thu, 16 Apr 2020 05:47:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:47:31: #3 Pre-compute pvalue-qvalue table... 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 05:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.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 05:47:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:47:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:47:40: 1000000 INFO @ Thu, 16 Apr 2020 05:47:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:47:45: 2000000 INFO @ Thu, 16 Apr 2020 05:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.05_summits.bed INFO @ Thu, 16 Apr 2020 05:47:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1567 records, 4 fields): 408 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:47:51: 3000000 INFO @ Thu, 16 Apr 2020 05:47:56: 4000000 INFO @ Thu, 16 Apr 2020 05:47:58: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 05:47:58: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 05:47:58: #1 total tags in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:47:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:47:58: #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 05:47:58: #1 tags after filtering in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:47:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:47:58: #1 finished! INFO @ Thu, 16 Apr 2020 05:47:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:47:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:47:59: #2 number of paired peaks: 515 WARNING @ Thu, 16 Apr 2020 05:47:59: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Thu, 16 Apr 2020 05:47:59: start model_add_line... INFO @ Thu, 16 Apr 2020 05:47:59: start X-correlation... INFO @ Thu, 16 Apr 2020 05:47:59: end of X-cor INFO @ Thu, 16 Apr 2020 05:47:59: #2 finished! INFO @ Thu, 16 Apr 2020 05:47:59: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 05:47:59: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 05:47:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10_model.r INFO @ Thu, 16 Apr 2020 05:47:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:47:59: #3 Pre-compute pvalue-qvalue table... 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 05:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.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 05:48:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:48:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:48:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:48:11: 1000000 INFO @ Thu, 16 Apr 2020 05:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.10_summits.bed INFO @ Thu, 16 Apr 2020 05:48:13: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1084 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:48:17: 2000000 INFO @ Thu, 16 Apr 2020 05:48:22: 3000000 INFO @ Thu, 16 Apr 2020 05:48:28: 4000000 INFO @ Thu, 16 Apr 2020 05:48:30: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 05:48:30: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 05:48:30: #1 total tags in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:48:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:48:30: #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 05:48:30: #1 tags after filtering in treatment: 4457923 INFO @ Thu, 16 Apr 2020 05:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:48:30: #1 finished! INFO @ Thu, 16 Apr 2020 05:48:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:48:30: #2 number of paired peaks: 515 WARNING @ Thu, 16 Apr 2020 05:48:30: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Thu, 16 Apr 2020 05:48:30: start model_add_line... INFO @ Thu, 16 Apr 2020 05:48:31: start X-correlation... INFO @ Thu, 16 Apr 2020 05:48:31: end of X-cor INFO @ Thu, 16 Apr 2020 05:48:31: #2 finished! INFO @ Thu, 16 Apr 2020 05:48:31: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 05:48:31: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 05:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20_model.r INFO @ Thu, 16 Apr 2020 05:48:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:48:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780074/SRX6780074.20_summits.bed INFO @ Thu, 16 Apr 2020 05:48:45: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (728 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。