Job ID = 5790821 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,051,425 reads read : 2,051,425 reads written : 2,051,425 spots read : 1,932,304 reads read : 1,932,304 reads written : 1,932,304 2020-04-21T22:42:47 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 ) 2020-04-21T22:42:47 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 ) 2020-04-21T22:42:47 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 : 1,903,092 reads read : 1,903,092 reads written : 1,903,092 spots read : 1,848,225 reads read : 1,848,225 reads written : 1,848,225 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: 00:01:11 7735046 reads; of these: 7735046 (100.00%) were unpaired; of these: 165582 (2.14%) aligned 0 times 6187034 (79.99%) aligned exactly 1 time 1382430 (17.87%) aligned >1 times 97.86% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 7350081 / 7569464 = 0.9710 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 07:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.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 07:48:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:48:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:48:55: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:48:55: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:48:55: #1 total tags in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:48:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:48:55: #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 07:48:55: #1 tags after filtering in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:48:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:55: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:55: #2 number of paired peaks: 416 WARNING @ Wed, 22 Apr 2020 07:48:55: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Wed, 22 Apr 2020 07:48:55: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:55: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:55: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:55: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:55: #2 predicted fragment length is 186 bps INFO @ Wed, 22 Apr 2020 07:48:55: #2 alternative fragment length(s) may be 127,186,208,258,342,418,450,513,590 bps INFO @ Wed, 22 Apr 2020 07:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05_model.r INFO @ Wed, 22 Apr 2020 07:48:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.05_summits.bed INFO @ Wed, 22 Apr 2020 07:48:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (143 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 07:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.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 07:49:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:49:25: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:49:25: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:49:25: #1 total tags in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:49:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:25: #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 07:49:25: #1 tags after filtering in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:25: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:25: #2 number of paired peaks: 416 WARNING @ Wed, 22 Apr 2020 07:49:25: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Wed, 22 Apr 2020 07:49:25: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:25: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:25: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:25: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:25: #2 predicted fragment length is 186 bps INFO @ Wed, 22 Apr 2020 07:49:25: #2 alternative fragment length(s) may be 127,186,208,258,342,418,450,513,590 bps INFO @ Wed, 22 Apr 2020 07:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10_model.r INFO @ Wed, 22 Apr 2020 07:49:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.10_summits.bed INFO @ Wed, 22 Apr 2020 07:49:26: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (43 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 INFO @ Wed, 22 Apr 2020 07:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.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 07:49:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:54: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:49:55: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:49:55: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:49:55: #1 total tags in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:49:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:55: #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 07:49:55: #1 tags after filtering in treatment: 219383 INFO @ Wed, 22 Apr 2020 07:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:55: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:55: #2 number of paired peaks: 416 WARNING @ Wed, 22 Apr 2020 07:49:55: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Wed, 22 Apr 2020 07:49:55: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:55: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:55: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:55: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:55: #2 predicted fragment length is 186 bps INFO @ Wed, 22 Apr 2020 07:49:55: #2 alternative fragment length(s) may be 127,186,208,258,342,418,450,513,590 bps INFO @ Wed, 22 Apr 2020 07:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20_model.r INFO @ Wed, 22 Apr 2020 07:49:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 07:49:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858299/ERX2858299.20_summits.bed INFO @ Wed, 22 Apr 2020 07:49:56: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis CompletedMACS2peakCalling