Job ID = 2007732 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:24:02 fasterq-dump.2.9.6 err: index.c get_nearest_offset() -> too many rounds pos = 24 of 40 2019-07-05T07:24:41 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 : 13,863 reads read : 27,726 reads written : 27,726 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: 00:00:01 13863 reads; of these: 13863 (100.00%) were paired; of these: 1326 (9.57%) aligned concordantly 0 times 11319 (81.65%) aligned concordantly exactly 1 time 1218 (8.79%) aligned concordantly >1 times ---- 1326 pairs aligned concordantly 0 times; of these: 342 (25.79%) aligned discordantly 1 time ---- 984 pairs aligned 0 times concordantly or discordantly; of these: 1968 mates make up the pairs; of these: 1685 (85.62%) aligned 0 times 168 (8.54%) aligned exactly 1 time 115 (5.84%) aligned >1 times 93.92% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 17 / 12794 = 0.0013 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.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 @ Fri, 05 Jul 2019 16:25:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:00: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:25:00: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:25:00: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:25:00: #1 total tags in treatment: 12520 INFO @ Fri, 05 Jul 2019 16:25:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:25:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:25:00: #1 tags after filtering in treatment: 12514 INFO @ Fri, 05 Jul 2019 16:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:25:00: #1 finished! INFO @ Fri, 05 Jul 2019 16:25:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:25:00: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:25:00: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:25:00: start model_add_line... INFO @ Fri, 05 Jul 2019 16:25:00: start X-correlation... INFO @ Fri, 05 Jul 2019 16:25:00: end of X-cor INFO @ Fri, 05 Jul 2019 16:25:00: #2 finished! INFO @ Fri, 05 Jul 2019 16:25:00: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 16:25:00: #2 alternative fragment length(s) may be 16,33,48,106,127,148,166,205,241,281,294,310,341,358,385,433,469,558,576 bps INFO @ Fri, 05 Jul 2019 16:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05_model.r INFO @ Fri, 05 Jul 2019 16:25:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:25:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.05_summits.bed INFO @ Fri, 05 Jul 2019 16:25:00: Done! pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.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 @ Fri, 05 Jul 2019 16:25:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:25:01: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:25:01: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:25:01: #1 total tags in treatment: 12520 INFO @ Fri, 05 Jul 2019 16:25:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:25:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:25:01: #1 tags after filtering in treatment: 12514 INFO @ Fri, 05 Jul 2019 16:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:25:01: #1 finished! INFO @ Fri, 05 Jul 2019 16:25:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:25:01: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:25:01: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:25:01: start model_add_line... INFO @ Fri, 05 Jul 2019 16:25:01: start X-correlation... INFO @ Fri, 05 Jul 2019 16:25:01: end of X-cor INFO @ Fri, 05 Jul 2019 16:25:01: #2 finished! INFO @ Fri, 05 Jul 2019 16:25:01: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 16:25:01: #2 alternative fragment length(s) may be 16,33,48,106,127,148,166,205,241,281,294,310,341,358,385,433,469,558,576 bps INFO @ Fri, 05 Jul 2019 16:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10_model.r INFO @ Fri, 05 Jul 2019 16:25:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:25:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.10_summits.bed INFO @ Fri, 05 Jul 2019 16:25:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.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 @ Fri, 05 Jul 2019 16:25:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:25:02: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:25:02: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:25:02: #1 total tags in treatment: 12520 INFO @ Fri, 05 Jul 2019 16:25:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:25:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:25:02: #1 tags after filtering in treatment: 12514 INFO @ Fri, 05 Jul 2019 16:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:25:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:25:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:25:02: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:25:02: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:25:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:25:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:25:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:25:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:25:02: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 16:25:02: #2 alternative fragment length(s) may be 16,33,48,106,127,148,166,205,241,281,294,310,341,358,385,433,469,558,576 bps INFO @ Fri, 05 Jul 2019 16:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20_model.r INFO @ Fri, 05 Jul 2019 16:25:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:25:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433680/ERX433680.20_summits.bed INFO @ Fri, 05 Jul 2019 16:25:02: Done! pass1 - making usageList (0 chroms): 122 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling