Job ID = 2640530 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:27:54 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 ) 2019-08-24T08:27:54 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.43' 2019-08-24T08:27:54 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 '172.19.7.43' 2019-08-24T08:27:54 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/008373/SRR8574061' 2019-08-24T08:27:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8574061' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:27:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:30:16 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 ) 2019-08-24T08:35:21 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 : 23,363,590 reads read : 46,727,180 reads written : 23,363,590 reads 0-length : 23,363,590 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:51 23363590 reads; of these: 23363590 (100.00%) were unpaired; of these: 586479 (2.51%) aligned 0 times 19306071 (82.63%) aligned exactly 1 time 3471040 (14.86%) aligned >1 times 97.49% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4596821 / 22777111 = 0.2018 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 24 Aug 2019 18:05:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:16: 1000000 INFO @ Sat, 24 Aug 2019 18:05:23: 2000000 INFO @ Sat, 24 Aug 2019 18:05:30: 3000000 INFO @ Sat, 24 Aug 2019 18:05:38: 4000000 INFO @ Sat, 24 Aug 2019 18:05:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 24 Aug 2019 18:05:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:45: 5000000 INFO @ Sat, 24 Aug 2019 18:05:47: 1000000 INFO @ Sat, 24 Aug 2019 18:05:52: 6000000 INFO @ Sat, 24 Aug 2019 18:05:56: 2000000 INFO @ Sat, 24 Aug 2019 18:05:59: 7000000 INFO @ Sat, 24 Aug 2019 18:06:05: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:06:07: 8000000 INFO @ Sat, 24 Aug 2019 18:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 24 Aug 2019 18:06:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:06:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:06:14: 4000000 INFO @ Sat, 24 Aug 2019 18:06:15: 9000000 INFO @ Sat, 24 Aug 2019 18:06:16: 1000000 INFO @ Sat, 24 Aug 2019 18:06:22: 10000000 INFO @ Sat, 24 Aug 2019 18:06:23: 5000000 INFO @ Sat, 24 Aug 2019 18:06:25: 2000000 INFO @ Sat, 24 Aug 2019 18:06:30: 11000000 INFO @ Sat, 24 Aug 2019 18:06:32: 6000000 INFO @ Sat, 24 Aug 2019 18:06:33: 3000000 INFO @ Sat, 24 Aug 2019 18:06:38: 12000000 INFO @ Sat, 24 Aug 2019 18:06:41: 4000000 INFO @ Sat, 24 Aug 2019 18:06:41: 7000000 INFO @ Sat, 24 Aug 2019 18:06:45: 13000000 INFO @ Sat, 24 Aug 2019 18:06:49: 5000000 INFO @ Sat, 24 Aug 2019 18:06:50: 8000000 INFO @ Sat, 24 Aug 2019 18:06:53: 14000000 INFO @ Sat, 24 Aug 2019 18:06:57: 6000000 INFO @ Sat, 24 Aug 2019 18:06:59: 9000000 INFO @ Sat, 24 Aug 2019 18:07:01: 15000000 INFO @ Sat, 24 Aug 2019 18:07:05: 7000000 INFO @ Sat, 24 Aug 2019 18:07:08: 10000000 INFO @ Sat, 24 Aug 2019 18:07:08: 16000000 INFO @ Sat, 24 Aug 2019 18:07:13: 8000000 INFO @ Sat, 24 Aug 2019 18:07:16: 17000000 INFO @ Sat, 24 Aug 2019 18:07:17: 11000000 INFO @ Sat, 24 Aug 2019 18:07:21: 9000000 INFO @ Sat, 24 Aug 2019 18:07:24: 18000000 INFO @ Sat, 24 Aug 2019 18:07:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:07:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:07:26: #1 total tags in treatment: 18180290 INFO @ Sat, 24 Aug 2019 18:07:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:07:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:07:26: 12000000 INFO @ Sat, 24 Aug 2019 18:07:26: #1 tags after filtering in treatment: 18180043 INFO @ Sat, 24 Aug 2019 18:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:07:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:07:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:07:29: 10000000 INFO @ Sat, 24 Aug 2019 18:07:31: #2 number of paired peaks: 76023 INFO @ Sat, 24 Aug 2019 18:07:31: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:32: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:32: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:32: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:32: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 18:07:32: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 18:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05_model.r INFO @ Sat, 24 Aug 2019 18:07:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:35: 13000000 INFO @ Sat, 24 Aug 2019 18:07:38: 11000000 INFO @ Sat, 24 Aug 2019 18:07:44: 14000000 INFO @ Sat, 24 Aug 2019 18:07:46: 12000000 INFO @ Sat, 24 Aug 2019 18:07:53: 15000000 INFO @ Sat, 24 Aug 2019 18:07:54: 13000000 INFO @ Sat, 24 Aug 2019 18:08:02: 16000000 INFO @ Sat, 24 Aug 2019 18:08:02: 14000000 INFO @ Sat, 24 Aug 2019 18:08:10: 15000000 INFO @ Sat, 24 Aug 2019 18:08:11: 17000000 INFO @ Sat, 24 Aug 2019 18:08:18: 16000000 INFO @ Sat, 24 Aug 2019 18:08:20: 18000000 INFO @ Sat, 24 Aug 2019 18:08:22: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:08:22: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:08:22: #1 total tags in treatment: 18180290 INFO @ Sat, 24 Aug 2019 18:08:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:08:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:08:22: #1 tags after filtering in treatment: 18180043 INFO @ Sat, 24 Aug 2019 18:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:08:22: #1 finished! INFO @ Sat, 24 Aug 2019 18:08:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:08:26: 17000000 INFO @ Sat, 24 Aug 2019 18:08:27: #2 number of paired peaks: 76023 INFO @ Sat, 24 Aug 2019 18:08:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:08:28: start X-correlation... INFO @ Sat, 24 Aug 2019 18:08:28: end of X-cor INFO @ Sat, 24 Aug 2019 18:08:28: #2 finished! INFO @ Sat, 24 Aug 2019 18:08:28: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 18:08:28: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 18:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10_model.r INFO @ Sat, 24 Aug 2019 18:08:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:08:30: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:34: 18000000 INFO @ Sat, 24 Aug 2019 18:08:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:08:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:08:36: #1 total tags in treatment: 18180290 INFO @ Sat, 24 Aug 2019 18:08:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:08:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:08:36: #1 tags after filtering in treatment: 18180043 INFO @ Sat, 24 Aug 2019 18:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:08:36: #1 finished! INFO @ Sat, 24 Aug 2019 18:08:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:08:42: #2 number of paired peaks: 76023 INFO @ Sat, 24 Aug 2019 18:08:42: start model_add_line... INFO @ Sat, 24 Aug 2019 18:08:42: start X-correlation... INFO @ Sat, 24 Aug 2019 18:08:42: end of X-cor INFO @ Sat, 24 Aug 2019 18:08:42: #2 finished! INFO @ Sat, 24 Aug 2019 18:08:42: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 18:08:42: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 24 Aug 2019 18:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20_model.r INFO @ Sat, 24 Aug 2019 18:08:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.05_summits.bed INFO @ Sat, 24 Aug 2019 18:09:02: Done! pass1 - making usageList (138 chroms): 15 millis pass2 - checking and writing primary data (46618 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:09:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:09:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.10_summits.bed INFO @ Sat, 24 Aug 2019 18:10:00: Done! pass1 - making usageList (107 chroms): 12 millis pass2 - checking and writing primary data (33804 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375006/SRX5375006.20_summits.bed INFO @ Sat, 24 Aug 2019 18:10:11: Done! pass1 - making usageList (79 chroms): 4 millis pass2 - checking and writing primary data (20054 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。