Job ID = 5790817 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,590,698 reads read : 1,590,698 reads written : 1,590,698 spots read : 1,509,178 reads read : 1,509,178 reads written : 1,509,178 2020-04-21T22:40:38 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 ) 2020-04-21T22:40:38 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 ) 2020-04-21T22:40:38 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 : 1,503,038 reads read : 1,503,038 reads written : 1,503,038 spots read : 1,444,906 reads read : 1,444,906 reads written : 1,444,906 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: 00:00:57 6047820 reads; of these: 6047820 (100.00%) were unpaired; of these: 117687 (1.95%) aligned 0 times 4727723 (78.17%) aligned exactly 1 time 1202410 (19.88%) aligned >1 times 98.05% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 5770885 / 5930133 = 0.9731 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 @ Wed, 22 Apr 2020 07:45:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:45:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:45:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:45:32: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:45:32: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:45:32: #1 total tags in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:45:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:45:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:45:32: #1 tags after filtering in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:45:32: #1 finished! INFO @ Wed, 22 Apr 2020 07:45:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:45:32: #2 number of paired peaks: 382 WARNING @ Wed, 22 Apr 2020 07:45:32: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Wed, 22 Apr 2020 07:45:32: start model_add_line... INFO @ Wed, 22 Apr 2020 07:45:32: start X-correlation... INFO @ Wed, 22 Apr 2020 07:45:32: end of X-cor INFO @ Wed, 22 Apr 2020 07:45:32: #2 finished! INFO @ Wed, 22 Apr 2020 07:45:32: #2 predicted fragment length is 261 bps INFO @ Wed, 22 Apr 2020 07:45:32: #2 alternative fragment length(s) may be 64,219,239,261,280,309 bps INFO @ Wed, 22 Apr 2020 07:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05_model.r INFO @ Wed, 22 Apr 2020 07:45:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:45:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.05_summits.bed INFO @ Wed, 22 Apr 2020 07:45:33: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 07:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:46:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:46:02: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:46:02: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:46:02: #1 total tags in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:46:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:46:02: #1 tags after filtering in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:46:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:46:02: #1 finished! INFO @ Wed, 22 Apr 2020 07:46:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:46:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:46:02: #2 number of paired peaks: 382 WARNING @ Wed, 22 Apr 2020 07:46:02: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Wed, 22 Apr 2020 07:46:02: start model_add_line... INFO @ Wed, 22 Apr 2020 07:46:02: start X-correlation... INFO @ Wed, 22 Apr 2020 07:46:02: end of X-cor INFO @ Wed, 22 Apr 2020 07:46:02: #2 finished! INFO @ Wed, 22 Apr 2020 07:46:02: #2 predicted fragment length is 261 bps INFO @ Wed, 22 Apr 2020 07:46:02: #2 alternative fragment length(s) may be 64,219,239,261,280,309 bps INFO @ Wed, 22 Apr 2020 07:46:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10_model.r INFO @ Wed, 22 Apr 2020 07:46:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:46:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.10_summits.bed INFO @ Wed, 22 Apr 2020 07:46:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:46:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:31: #1 read treatment tags... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 07:46:32: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:46:32: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:46:32: #1 total tags in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:46:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:46:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:46:32: #1 tags after filtering in treatment: 159248 INFO @ Wed, 22 Apr 2020 07:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:46:32: #1 finished! INFO @ Wed, 22 Apr 2020 07:46:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:46:32: #2 number of paired peaks: 382 WARNING @ Wed, 22 Apr 2020 07:46:32: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Wed, 22 Apr 2020 07:46:32: start model_add_line... INFO @ Wed, 22 Apr 2020 07:46:32: start X-correlation... INFO @ Wed, 22 Apr 2020 07:46:32: end of X-cor INFO @ Wed, 22 Apr 2020 07:46:32: #2 finished! INFO @ Wed, 22 Apr 2020 07:46:32: #2 predicted fragment length is 261 bps INFO @ Wed, 22 Apr 2020 07:46:32: #2 alternative fragment length(s) may be 64,219,239,261,280,309 bps INFO @ Wed, 22 Apr 2020 07:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20_model.r INFO @ Wed, 22 Apr 2020 07:46:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:46:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858296/ERX2858296.20_summits.bed INFO @ Wed, 22 Apr 2020 07:46:33: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling