Job ID = 2007896 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:39:35 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 ) 2019-07-05T07:40:03 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 : 178,198 reads read : 356,396 reads written : 356,396 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: 00:00:06 178198 reads; of these: 178198 (100.00%) were paired; of these: 19438 (10.91%) aligned concordantly 0 times 145725 (81.78%) aligned concordantly exactly 1 time 13035 (7.31%) aligned concordantly >1 times ---- 19438 pairs aligned concordantly 0 times; of these: 11564 (59.49%) aligned discordantly 1 time ---- 7874 pairs aligned 0 times concordantly or discordantly; of these: 15748 mates make up the pairs; of these: 10455 (66.39%) aligned 0 times 2923 (18.56%) aligned exactly 1 time 2370 (15.05%) aligned >1 times 97.07% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 500 / 167713 = 0.0030 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 16:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.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 16:40:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:40:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.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 16:40:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:40:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.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 16:40:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:40:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:40:32: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:40:32: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:40:32: #1 total tags in treatment: 158279 INFO @ Fri, 05 Jul 2019 16:40:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:40:32: #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 16:40:32: #1 tags after filtering in treatment: 156724 INFO @ Fri, 05 Jul 2019 16:40:32: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:40:32: #1 finished! INFO @ Fri, 05 Jul 2019 16:40:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:40:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:40:32: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 16:40:32: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 16:40:32: start model_add_line... INFO @ Fri, 05 Jul 2019 16:40:32: start X-correlation... INFO @ Fri, 05 Jul 2019 16:40:32: end of X-cor INFO @ Fri, 05 Jul 2019 16:40:32: #2 finished! INFO @ Fri, 05 Jul 2019 16:40:32: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 16:40:32: #2 alternative fragment length(s) may be 3,77,113,141,180,216 bps INFO @ Fri, 05 Jul 2019 16:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05_model.r INFO @ Fri, 05 Jul 2019 16:40:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:40:33: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:40:33: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:40:33: #1 total tags in treatment: 158279 INFO @ Fri, 05 Jul 2019 16:40:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:40:33: #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 16:40:33: #1 tags after filtering in treatment: 156724 INFO @ Fri, 05 Jul 2019 16:40:33: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:40:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:40:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:40:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:40:33: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 16:40:33: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 16:40:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:40:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:40:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:40:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:40:33: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 16:40:33: #2 alternative fragment length(s) may be 3,77,113,141,180,216 bps INFO @ Fri, 05 Jul 2019 16:40:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10_model.r INFO @ Fri, 05 Jul 2019 16:40:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.05_summits.bed INFO @ Fri, 05 Jul 2019 16:40:33: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:40:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:40:33: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:40:33: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:40:33: #1 total tags in treatment: 158279 INFO @ Fri, 05 Jul 2019 16:40:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:40:33: #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 16:40:33: #1 tags after filtering in treatment: 156724 INFO @ Fri, 05 Jul 2019 16:40:33: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:40:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:40:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:40:33: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 16:40:33: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 16:40:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:40:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:40:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:40:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:40:33: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 16:40:33: #2 alternative fragment length(s) may be 3,77,113,141,180,216 bps INFO @ Fri, 05 Jul 2019 16:40:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20_model.r INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:40:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:40:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.10_summits.bed INFO @ Fri, 05 Jul 2019 16:40:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:40:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462430/ERX462430.20_summits.bed INFO @ Fri, 05 Jul 2019 16:40:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 0 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling