Job ID = 2011830 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:51:54 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 ) 2019-07-05T17:52:02 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 ) 2019-07-05T17:52:02 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 ) 2019-07-05T17:52:02 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 : 14,166,477 reads read : 28,332,954 reads written : 28,332,954 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: 00:14:05 14166477 reads; of these: 14166477 (100.00%) were paired; of these: 803593 (5.67%) aligned concordantly 0 times 10651247 (75.19%) aligned concordantly exactly 1 time 2711637 (19.14%) aligned concordantly >1 times ---- 803593 pairs aligned concordantly 0 times; of these: 5157 (0.64%) aligned discordantly 1 time ---- 798436 pairs aligned 0 times concordantly or discordantly; of these: 1596872 mates make up the pairs; of these: 1411241 (88.38%) aligned 0 times 124496 (7.80%) aligned exactly 1 time 61135 (3.83%) aligned >1 times 95.02% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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_sort_core] merging from 12 files... [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] 11899154 / 13366776 = 0.8902 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 03:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.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 03:21:36: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:36: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.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 03:21:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.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 03:21:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:48: 1000000 INFO @ Sat, 06 Jul 2019 03:21:49: 1000000 INFO @ Sat, 06 Jul 2019 03:21:49: 1000000 INFO @ Sat, 06 Jul 2019 03:21:59: 2000000 INFO @ Sat, 06 Jul 2019 03:22:00: 2000000 INFO @ Sat, 06 Jul 2019 03:22:01: 2000000 INFO @ Sat, 06 Jul 2019 03:22:10: 3000000 INFO @ Sat, 06 Jul 2019 03:22:11: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:22:11: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:22:11: #1 total tags in treatment: 1466621 INFO @ Sat, 06 Jul 2019 03:22:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:11: #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 03:22:11: #1 tags after filtering in treatment: 1097688 INFO @ Sat, 06 Jul 2019 03:22:11: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:22:11: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:11: #2 number of paired peaks: 244 WARNING @ Sat, 06 Jul 2019 03:22:11: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:11: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:11: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:11: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:11: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:11: #2 predicted fragment length is 267 bps INFO @ Sat, 06 Jul 2019 03:22:11: #2 alternative fragment length(s) may be 3,267,282,593 bps INFO @ Sat, 06 Jul 2019 03:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20_model.r INFO @ Sat, 06 Jul 2019 03:22:11: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:12: 3000000 INFO @ Sat, 06 Jul 2019 03:22:14: 3000000 INFO @ Sat, 06 Jul 2019 03:22:14: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:22:14: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:22:14: #1 total tags in treatment: 1466621 INFO @ Sat, 06 Jul 2019 03:22:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:14: #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 03:22:14: #1 tags after filtering in treatment: 1097688 INFO @ Sat, 06 Jul 2019 03:22:14: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:22:14: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:14: #2 number of paired peaks: 244 WARNING @ Sat, 06 Jul 2019 03:22:14: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:14: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:14: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:14: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:14: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:14: #2 predicted fragment length is 267 bps INFO @ Sat, 06 Jul 2019 03:22:14: #2 alternative fragment length(s) may be 3,267,282,593 bps INFO @ Sat, 06 Jul 2019 03:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05_model.r INFO @ Sat, 06 Jul 2019 03:22:14: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:15: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:22:15: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:22:15: #1 total tags in treatment: 1466621 INFO @ Sat, 06 Jul 2019 03:22:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:15: #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 03:22:15: #1 tags after filtering in treatment: 1097688 INFO @ Sat, 06 Jul 2019 03:22:15: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:22:15: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:15: #2 number of paired peaks: 244 WARNING @ Sat, 06 Jul 2019 03:22:15: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:15: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:15: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:15: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:15: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:15: #2 predicted fragment length is 267 bps INFO @ Sat, 06 Jul 2019 03:22:15: #2 alternative fragment length(s) may be 3,267,282,593 bps INFO @ Sat, 06 Jul 2019 03:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10_model.r INFO @ Sat, 06 Jul 2019 03:22:16: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20_peaks.xls BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 03:22:19: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05_peaks.xls BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.20_summits.bed INFO @ Sat, 06 Jul 2019 03:22:47: Done! INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.05_summits.bed INFO @ Sat, 06 Jul 2019 03:22:47: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:47: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 3 millis pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:22:52: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126588/SRX5126588.10_summits.bed INFO @ Sat, 06 Jul 2019 03:22:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。