Job ID = 1294311 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:19:51 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 ) 2019-06-02T21:19:51 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 ) 2019-06-02T21:19:51 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 ) 2019-06-02T21:20:01 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 ) 2019-06-02T21:21:20 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T21:21:50 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 ) 2019-06-02T21:21:50 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.15' 2019-06-02T21:21:50 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' (130.14.250.27) from '172.19.7.15' 2019-06-02T21:21:50 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 ) 2019-06-02T21:21:50 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.15' 2019-06-02T21:21:50 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' (130.14.250.27) from '172.19.7.15' 2019-06-02T21:22:45 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 ) 2019-06-02T21:22:45 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.15' 2019-06-02T21:22:45 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' (130.14.250.27) from '172.19.7.15' 2019-06-02T21:22:45 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra44/SRR/004990/SRR5110254' (130.14.250.27), 32768) from '172.19.7.15' 2019-06-02T21:22:45 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 ) 2019-06-02T21:22:45 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.15' 2019-06-02T21:22:45 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' (130.14.250.27) from '172.19.7.15' 2019-06-02T21:22:45 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra44/SRR/004990/SRR5110254' (130.14.250.27), 32768) from '172.19.7.15' spots read : 17,754,733 reads read : 17,754,733 reads written : 17,754,733 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:09:08 17754733 reads; of these: 17754733 (100.00%) were unpaired; of these: 393265 (2.21%) aligned 0 times 11873317 (66.87%) aligned exactly 1 time 5488151 (30.91%) aligned >1 times 97.79% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1451269 / 17361468 = 0.0836 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 @ Mon, 03 Jun 2019 06:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 06:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:39: 1000000 INFO @ Mon, 03 Jun 2019 06:40:39: 1000000 INFO @ Mon, 03 Jun 2019 06:40:39: 1000000 INFO @ Mon, 03 Jun 2019 06:40:47: 2000000 INFO @ Mon, 03 Jun 2019 06:40:48: 2000000 INFO @ Mon, 03 Jun 2019 06:40:50: 2000000 INFO @ Mon, 03 Jun 2019 06:40:56: 3000000 INFO @ Mon, 03 Jun 2019 06:40:56: 3000000 INFO @ Mon, 03 Jun 2019 06:40:59: 3000000 INFO @ Mon, 03 Jun 2019 06:41:04: 4000000 INFO @ Mon, 03 Jun 2019 06:41:05: 4000000 INFO @ Mon, 03 Jun 2019 06:41:09: 4000000 INFO @ Mon, 03 Jun 2019 06:41:12: 5000000 INFO @ Mon, 03 Jun 2019 06:41:13: 5000000 INFO @ Mon, 03 Jun 2019 06:41:19: 5000000 INFO @ Mon, 03 Jun 2019 06:41:20: 6000000 INFO @ Mon, 03 Jun 2019 06:41:21: 6000000 INFO @ Mon, 03 Jun 2019 06:41:28: 7000000 INFO @ Mon, 03 Jun 2019 06:41:28: 6000000 INFO @ Mon, 03 Jun 2019 06:41:29: 7000000 INFO @ Mon, 03 Jun 2019 06:41:37: 8000000 INFO @ Mon, 03 Jun 2019 06:41:37: 7000000 INFO @ Mon, 03 Jun 2019 06:41:38: 8000000 INFO @ Mon, 03 Jun 2019 06:41:45: 9000000 INFO @ Mon, 03 Jun 2019 06:41:47: 9000000 INFO @ Mon, 03 Jun 2019 06:41:48: 8000000 INFO @ Mon, 03 Jun 2019 06:41:53: 10000000 INFO @ Mon, 03 Jun 2019 06:41:55: 10000000 INFO @ Mon, 03 Jun 2019 06:41:57: 9000000 INFO @ Mon, 03 Jun 2019 06:42:01: 11000000 INFO @ Mon, 03 Jun 2019 06:42:04: 11000000 INFO @ Mon, 03 Jun 2019 06:42:07: 10000000 INFO @ Mon, 03 Jun 2019 06:42:09: 12000000 INFO @ Mon, 03 Jun 2019 06:42:13: 12000000 INFO @ Mon, 03 Jun 2019 06:42:16: 11000000 INFO @ Mon, 03 Jun 2019 06:42:18: 13000000 INFO @ Mon, 03 Jun 2019 06:42:21: 13000000 INFO @ Mon, 03 Jun 2019 06:42:26: 14000000 INFO @ Mon, 03 Jun 2019 06:42:26: 12000000 INFO @ Mon, 03 Jun 2019 06:42:29: 14000000 INFO @ Mon, 03 Jun 2019 06:42:34: 15000000 INFO @ Mon, 03 Jun 2019 06:42:35: 13000000 INFO @ Mon, 03 Jun 2019 06:42:37: 15000000 INFO @ Mon, 03 Jun 2019 06:42:41: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:42:41: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:42:41: #1 total tags in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:42:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:42:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:42:42: #1 tags after filtering in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:42:42: #1 finished! INFO @ Mon, 03 Jun 2019 06:42:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:42:43: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 06:42:43: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 06:42:43: start model_add_line... INFO @ Mon, 03 Jun 2019 06:42:44: start X-correlation... INFO @ Mon, 03 Jun 2019 06:42:44: end of X-cor INFO @ Mon, 03 Jun 2019 06:42:44: #2 finished! INFO @ Mon, 03 Jun 2019 06:42:44: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 06:42:44: #2 alternative fragment length(s) may be 4,96 bps INFO @ Mon, 03 Jun 2019 06:42:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05_model.r WARNING @ Mon, 03 Jun 2019 06:42:44: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:42:44: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Mon, 03 Jun 2019 06:42:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:42:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:42:44: 14000000 INFO @ Mon, 03 Jun 2019 06:42:45: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:42:45: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:42:45: #1 total tags in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:42:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:42:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:42:45: #1 tags after filtering in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:42:45: #1 finished! INFO @ Mon, 03 Jun 2019 06:42:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:42:47: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 06:42:47: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 06:42:47: start model_add_line... INFO @ Mon, 03 Jun 2019 06:42:47: start X-correlation... INFO @ Mon, 03 Jun 2019 06:42:47: end of X-cor INFO @ Mon, 03 Jun 2019 06:42:47: #2 finished! INFO @ Mon, 03 Jun 2019 06:42:47: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 06:42:47: #2 alternative fragment length(s) may be 4,96 bps INFO @ Mon, 03 Jun 2019 06:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10_model.r WARNING @ Mon, 03 Jun 2019 06:42:47: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:42:47: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Mon, 03 Jun 2019 06:42:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:42:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:42:53: 15000000 INFO @ Mon, 03 Jun 2019 06:43:01: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:43:01: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:43:01: #1 total tags in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:43:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:43:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:43:02: #1 tags after filtering in treatment: 15910199 INFO @ Mon, 03 Jun 2019 06:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:43:02: #1 finished! INFO @ Mon, 03 Jun 2019 06:43:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:43:03: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 06:43:03: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 06:43:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:43:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:43:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:43:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:43:03: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 06:43:03: #2 alternative fragment length(s) may be 4,96 bps INFO @ Mon, 03 Jun 2019 06:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20_model.r WARNING @ Mon, 03 Jun 2019 06:43:03: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:43:03: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Mon, 03 Jun 2019 06:43:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:43:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:43:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:43:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:43:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.05_summits.bed INFO @ Mon, 03 Jun 2019 06:43:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4641 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.10_summits.bed INFO @ Mon, 03 Jun 2019 06:43:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2493 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422640/SRX2422640.20_summits.bed INFO @ Mon, 03 Jun 2019 06:44:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1252 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。