Job ID = 2011902 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T18:06:10 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 : 4,587,326 reads read : 9,174,652 reads written : 9,174,652 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: 00:03:08 4587326 reads; of these: 4587326 (100.00%) were paired; of these: 519216 (11.32%) aligned concordantly 0 times 3235933 (70.54%) aligned concordantly exactly 1 time 832177 (18.14%) aligned concordantly >1 times ---- 519216 pairs aligned concordantly 0 times; of these: 293745 (56.57%) aligned discordantly 1 time ---- 225471 pairs aligned 0 times concordantly or discordantly; of these: 450942 mates make up the pairs; of these: 209655 (46.49%) aligned 0 times 81209 (18.01%) aligned exactly 1 time 160078 (35.50%) aligned >1 times 97.71% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 175266 / 4359545 = 0.0402 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 @ Sat, 06 Jul 2019 03:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.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 @ Sat, 06 Jul 2019 03:14:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:14:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.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 @ Sat, 06 Jul 2019 03:15:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:15:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.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 @ Sat, 06 Jul 2019 03:15:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:15:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:15:07: 1000000 INFO @ Sat, 06 Jul 2019 03:15:08: 1000000 INFO @ Sat, 06 Jul 2019 03:15:08: 1000000 INFO @ Sat, 06 Jul 2019 03:15:13: 2000000 INFO @ Sat, 06 Jul 2019 03:15:15: 2000000 INFO @ Sat, 06 Jul 2019 03:15:16: 2000000 INFO @ Sat, 06 Jul 2019 03:15:19: 3000000 INFO @ Sat, 06 Jul 2019 03:15:22: 3000000 INFO @ Sat, 06 Jul 2019 03:15:24: 3000000 INFO @ Sat, 06 Jul 2019 03:15:25: 4000000 INFO @ Sat, 06 Jul 2019 03:15:29: 4000000 INFO @ Sat, 06 Jul 2019 03:15:31: 5000000 INFO @ Sat, 06 Jul 2019 03:15:32: 4000000 INFO @ Sat, 06 Jul 2019 03:15:35: 5000000 INFO @ Sat, 06 Jul 2019 03:15:37: 6000000 INFO @ Sat, 06 Jul 2019 03:15:40: 5000000 INFO @ Sat, 06 Jul 2019 03:15:42: 6000000 INFO @ Sat, 06 Jul 2019 03:15:43: 7000000 INFO @ Sat, 06 Jul 2019 03:15:48: 6000000 INFO @ Sat, 06 Jul 2019 03:15:49: 7000000 INFO @ Sat, 06 Jul 2019 03:15:49: 8000000 INFO @ Sat, 06 Jul 2019 03:15:52: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:15:52: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:15:52: #1 total tags in treatment: 3898798 INFO @ Sat, 06 Jul 2019 03:15:52: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:15:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:15:52: #1 tags after filtering in treatment: 2895977 INFO @ Sat, 06 Jul 2019 03:15:52: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:15:52: #1 finished! INFO @ Sat, 06 Jul 2019 03:15:52: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:15:53: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:15:53: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:15:53: start model_add_line... INFO @ Sat, 06 Jul 2019 03:15:53: start X-correlation... INFO @ Sat, 06 Jul 2019 03:15:53: end of X-cor INFO @ Sat, 06 Jul 2019 03:15:53: #2 finished! INFO @ Sat, 06 Jul 2019 03:15:53: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:15:53: #2 alternative fragment length(s) may be 0,51,109,164,166,179,240,258,274,295,304,317,335,383,445,464,515,536,580 bps INFO @ Sat, 06 Jul 2019 03:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10_model.r INFO @ Sat, 06 Jul 2019 03:15:54: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:15:55: 8000000 INFO @ Sat, 06 Jul 2019 03:15:56: 7000000 INFO @ Sat, 06 Jul 2019 03:15:59: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:15:59: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:15:59: #1 total tags in treatment: 3898798 INFO @ Sat, 06 Jul 2019 03:15:59: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:15:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:15:59: #1 tags after filtering in treatment: 2895977 INFO @ Sat, 06 Jul 2019 03:15:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:15:59: #1 finished! INFO @ Sat, 06 Jul 2019 03:15:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:16:00: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:16:00: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:16:00: start model_add_line... INFO @ Sat, 06 Jul 2019 03:16:00: start X-correlation... INFO @ Sat, 06 Jul 2019 03:16:00: end of X-cor INFO @ Sat, 06 Jul 2019 03:16:00: #2 finished! INFO @ Sat, 06 Jul 2019 03:16:00: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:16:00: #2 alternative fragment length(s) may be 0,51,109,164,166,179,240,258,274,295,304,317,335,383,445,464,515,536,580 bps INFO @ Sat, 06 Jul 2019 03:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20_model.r INFO @ Sat, 06 Jul 2019 03:16:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:16:02: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:16:04: 8000000 INFO @ Sat, 06 Jul 2019 03:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.10_summits.bed INFO @ Sat, 06 Jul 2019 03:16:05: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:16:07: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:16:08: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:16:08: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:16:08: #1 total tags in treatment: 3898798 INFO @ Sat, 06 Jul 2019 03:16:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:16:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:16:08: #1 tags after filtering in treatment: 2895977 INFO @ Sat, 06 Jul 2019 03:16:08: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 03:16:08: #1 finished! INFO @ Sat, 06 Jul 2019 03:16:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:16:08: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:16:08: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:16:08: start model_add_line... INFO @ Sat, 06 Jul 2019 03:16:08: start X-correlation... INFO @ Sat, 06 Jul 2019 03:16:08: end of X-cor INFO @ Sat, 06 Jul 2019 03:16:08: #2 finished! INFO @ Sat, 06 Jul 2019 03:16:08: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:16:08: #2 alternative fragment length(s) may be 0,51,109,164,166,179,240,258,274,295,304,317,335,383,445,464,515,536,580 bps INFO @ Sat, 06 Jul 2019 03:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05_model.r INFO @ Sat, 06 Jul 2019 03:16:09: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:16:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.20_summits.bed INFO @ Sat, 06 Jul 2019 03:16:10: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:16:16: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383675/SRX5383675.05_summits.bed INFO @ Sat, 06 Jul 2019 03:16:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。