Job ID = 2010604 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:32:27 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 ) 2019-07-05T14:32:58 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 ) 2019-07-05T14:36:33 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 ) 2019-07-05T14:36:34 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 ) 2019-07-05T14:36:34 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 ) 2019-07-05T14:38:20 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 ) 2019-07-05T14:38:20 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 ) 2019-07-05T14:38:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:38:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.90' 2019-07-05T14:38:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.90' 2019-07-05T14:41:50 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 : 6,121,673 reads read : 12,243,346 reads written : 12,243,346 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: 00:04:06 6121673 reads; of these: 6121673 (100.00%) were paired; of these: 2413341 (39.42%) aligned concordantly 0 times 3209904 (52.44%) aligned concordantly exactly 1 time 498428 (8.14%) aligned concordantly >1 times ---- 2413341 pairs aligned concordantly 0 times; of these: 15412 (0.64%) aligned discordantly 1 time ---- 2397929 pairs aligned 0 times concordantly or discordantly; of these: 4795858 mates make up the pairs; of these: 4547751 (94.83%) aligned 0 times 203081 (4.23%) aligned exactly 1 time 45026 (0.94%) aligned >1 times 62.86% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 266665 / 3718973 = 0.0717 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 23:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.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 23:49:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:49:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.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 23:50:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:50:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.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 23:50:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:50:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:10: 1000000 INFO @ Fri, 05 Jul 2019 23:50:11: 1000000 INFO @ Fri, 05 Jul 2019 23:50:12: 1000000 INFO @ Fri, 05 Jul 2019 23:50:21: 2000000 INFO @ Fri, 05 Jul 2019 23:50:21: 2000000 INFO @ Fri, 05 Jul 2019 23:50:24: 2000000 INFO @ Fri, 05 Jul 2019 23:50:30: 3000000 INFO @ Fri, 05 Jul 2019 23:50:31: 3000000 INFO @ Fri, 05 Jul 2019 23:50:35: 3000000 INFO @ Fri, 05 Jul 2019 23:50:41: 4000000 INFO @ Fri, 05 Jul 2019 23:50:42: 4000000 INFO @ Fri, 05 Jul 2019 23:50:45: 4000000 INFO @ Fri, 05 Jul 2019 23:50:50: 5000000 INFO @ Fri, 05 Jul 2019 23:50:52: 5000000 INFO @ Fri, 05 Jul 2019 23:50:57: 5000000 INFO @ Fri, 05 Jul 2019 23:51:00: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:51:02: 6000000 INFO @ Fri, 05 Jul 2019 23:51:07: 6000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:51:09: 7000000 INFO @ Fri, 05 Jul 2019 23:51:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:51:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:51:11: #1 total tags in treatment: 3442079 INFO @ Fri, 05 Jul 2019 23:51:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:11: #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 23:51:11: #1 tags after filtering in treatment: 1679215 INFO @ Fri, 05 Jul 2019 23:51:11: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:51:11: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:51:11: #2 number of paired peaks: 965 WARNING @ Fri, 05 Jul 2019 23:51:11: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:11: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:11: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:11: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:11: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:11: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:51:11: #2 alternative fragment length(s) may be 0,170,198,221,258,263 bps INFO @ Fri, 05 Jul 2019 23:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10_model.r INFO @ Fri, 05 Jul 2019 23:51:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:12: 7000000 INFO @ Fri, 05 Jul 2019 23:51:14: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:51:14: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:51:14: #1 total tags in treatment: 3442079 INFO @ Fri, 05 Jul 2019 23:51:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:14: #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 23:51:14: #1 tags after filtering in treatment: 1679215 INFO @ Fri, 05 Jul 2019 23:51:14: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:51:14: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:51:14: #2 number of paired peaks: 965 WARNING @ Fri, 05 Jul 2019 23:51:14: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:14: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:14: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:14: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:14: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:14: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:51:14: #2 alternative fragment length(s) may be 0,170,198,221,258,263 bps INFO @ Fri, 05 Jul 2019 23:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05_model.r INFO @ Fri, 05 Jul 2019 23:51:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:18: 7000000 INFO @ Fri, 05 Jul 2019 23:51:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:51:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:51:19: #1 total tags in treatment: 3442079 INFO @ Fri, 05 Jul 2019 23:51:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:19: #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 23:51:20: #1 tags after filtering in treatment: 1679215 INFO @ Fri, 05 Jul 2019 23:51:20: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:51:20: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:51:20: #2 number of paired peaks: 965 WARNING @ Fri, 05 Jul 2019 23:51:20: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:20: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:20: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:20: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:20: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:20: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:51:20: #2 alternative fragment length(s) may be 0,170,198,221,258,263 bps INFO @ Fri, 05 Jul 2019 23:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20_model.r INFO @ Fri, 05 Jul 2019 23:51:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.10_summits.bed INFO @ Fri, 05 Jul 2019 23:51:24: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (299 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:51:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.05_summits.bed INFO @ Fri, 05 Jul 2019 23:51:27: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (609 records, 4 fields): 98 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:51:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381304/SRX381304.20_summits.bed INFO @ Fri, 05 Jul 2019 23:51:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 3 millis CompletedMACS2peakCalling