Job ID = 2640404 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:03:06 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 ) 2019-08-24T07:03:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.10' 2019-08-24T07:03:06 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' (130.14.250.26) from '172.19.7.10' 2019-08-24T07:03:06 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/era16/ERR/ERR364/ERR364312' 2019-08-24T07:03:19 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR364312', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-08-24T07:05:51 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 ) spots read : 52,505,527 reads read : 52,505,527 reads written : 52,505,527 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: 00:36:44 52505527 reads; of these: 52505527 (100.00%) were unpaired; of these: 14481406 (27.58%) aligned 0 times 26368502 (50.22%) aligned exactly 1 time 11655619 (22.20%) aligned >1 times 72.42% overall alignment rate Time searching: 00:36:47 Overall time: 00:36:47 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 16 files... [bam_rmdupse_core] 10461321 / 38024121 = 0.2751 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.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 17:24:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:24:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:24:50: 1000000 INFO @ Sat, 24 Aug 2019 17:24:58: 2000000 INFO @ Sat, 24 Aug 2019 17:25:06: 3000000 INFO @ Sat, 24 Aug 2019 17:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.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 17:25:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:25:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:25:13: 4000000 INFO @ Sat, 24 Aug 2019 17:25:19: 1000000 INFO @ Sat, 24 Aug 2019 17:25:21: 5000000 INFO @ Sat, 24 Aug 2019 17:25:27: 2000000 INFO @ Sat, 24 Aug 2019 17:25:29: 6000000 INFO @ Sat, 24 Aug 2019 17:25:34: 3000000 INFO @ Sat, 24 Aug 2019 17:25:37: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:25:41: 4000000 INFO @ Sat, 24 Aug 2019 17:25:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.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 17:25:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:25:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:25:45: 8000000 INFO @ Sat, 24 Aug 2019 17:25:48: 5000000 INFO @ Sat, 24 Aug 2019 17:25:49: 1000000 INFO @ Sat, 24 Aug 2019 17:25:52: 9000000 INFO @ Sat, 24 Aug 2019 17:25:55: 6000000 INFO @ Sat, 24 Aug 2019 17:25:56: 2000000 INFO @ Sat, 24 Aug 2019 17:26:00: 10000000 INFO @ Sat, 24 Aug 2019 17:26:02: 7000000 INFO @ Sat, 24 Aug 2019 17:26:03: 3000000 INFO @ Sat, 24 Aug 2019 17:26:08: 11000000 INFO @ Sat, 24 Aug 2019 17:26:09: 8000000 INFO @ Sat, 24 Aug 2019 17:26:10: 4000000 INFO @ Sat, 24 Aug 2019 17:26:16: 12000000 INFO @ Sat, 24 Aug 2019 17:26:16: 9000000 INFO @ Sat, 24 Aug 2019 17:26:17: 5000000 INFO @ Sat, 24 Aug 2019 17:26:23: 10000000 INFO @ Sat, 24 Aug 2019 17:26:24: 13000000 INFO @ Sat, 24 Aug 2019 17:26:24: 6000000 INFO @ Sat, 24 Aug 2019 17:26:30: 11000000 INFO @ Sat, 24 Aug 2019 17:26:31: 7000000 INFO @ Sat, 24 Aug 2019 17:26:32: 14000000 INFO @ Sat, 24 Aug 2019 17:26:38: 12000000 INFO @ Sat, 24 Aug 2019 17:26:39: 8000000 INFO @ Sat, 24 Aug 2019 17:26:39: 15000000 INFO @ Sat, 24 Aug 2019 17:26:44: 13000000 INFO @ Sat, 24 Aug 2019 17:26:45: 9000000 INFO @ Sat, 24 Aug 2019 17:26:47: 16000000 INFO @ Sat, 24 Aug 2019 17:26:51: 14000000 INFO @ Sat, 24 Aug 2019 17:26:53: 10000000 INFO @ Sat, 24 Aug 2019 17:26:55: 17000000 INFO @ Sat, 24 Aug 2019 17:26:58: 15000000 INFO @ Sat, 24 Aug 2019 17:26:59: 11000000 INFO @ Sat, 24 Aug 2019 17:27:03: 18000000 INFO @ Sat, 24 Aug 2019 17:27:05: 16000000 INFO @ Sat, 24 Aug 2019 17:27:06: 12000000 INFO @ Sat, 24 Aug 2019 17:27:11: 19000000 INFO @ Sat, 24 Aug 2019 17:27:12: 17000000 INFO @ Sat, 24 Aug 2019 17:27:13: 13000000 INFO @ Sat, 24 Aug 2019 17:27:19: 18000000 INFO @ Sat, 24 Aug 2019 17:27:19: 20000000 INFO @ Sat, 24 Aug 2019 17:27:20: 14000000 INFO @ Sat, 24 Aug 2019 17:27:26: 19000000 INFO @ Sat, 24 Aug 2019 17:27:27: 21000000 INFO @ Sat, 24 Aug 2019 17:27:27: 15000000 INFO @ Sat, 24 Aug 2019 17:27:33: 20000000 INFO @ Sat, 24 Aug 2019 17:27:34: 16000000 INFO @ Sat, 24 Aug 2019 17:27:35: 22000000 INFO @ Sat, 24 Aug 2019 17:27:40: 21000000 INFO @ Sat, 24 Aug 2019 17:27:42: 17000000 INFO @ Sat, 24 Aug 2019 17:27:43: 23000000 INFO @ Sat, 24 Aug 2019 17:27:47: 22000000 INFO @ Sat, 24 Aug 2019 17:27:49: 18000000 INFO @ Sat, 24 Aug 2019 17:27:51: 24000000 INFO @ Sat, 24 Aug 2019 17:27:54: 23000000 INFO @ Sat, 24 Aug 2019 17:27:56: 19000000 INFO @ Sat, 24 Aug 2019 17:27:59: 25000000 INFO @ Sat, 24 Aug 2019 17:28:01: 24000000 INFO @ Sat, 24 Aug 2019 17:28:03: 20000000 INFO @ Sat, 24 Aug 2019 17:28:07: 26000000 INFO @ Sat, 24 Aug 2019 17:28:08: 25000000 INFO @ Sat, 24 Aug 2019 17:28:10: 21000000 INFO @ Sat, 24 Aug 2019 17:28:15: 27000000 INFO @ Sat, 24 Aug 2019 17:28:16: 26000000 INFO @ Sat, 24 Aug 2019 17:28:18: 22000000 INFO @ Sat, 24 Aug 2019 17:28:20: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:28:20: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:28:20: #1 total tags in treatment: 27562800 INFO @ Sat, 24 Aug 2019 17:28:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:28:20: #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 17:28:21: #1 tags after filtering in treatment: 27562703 INFO @ Sat, 24 Aug 2019 17:28:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:28:21: #1 finished! INFO @ Sat, 24 Aug 2019 17:28:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:28:23: 27000000 INFO @ Sat, 24 Aug 2019 17:28:24: #2 number of paired peaks: 6706 INFO @ Sat, 24 Aug 2019 17:28:24: start model_add_line... INFO @ Sat, 24 Aug 2019 17:28:24: start X-correlation... INFO @ Sat, 24 Aug 2019 17:28:24: end of X-cor INFO @ Sat, 24 Aug 2019 17:28:24: #2 finished! INFO @ Sat, 24 Aug 2019 17:28:24: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:28:24: #2 alternative fragment length(s) may be 50,227,412,504 bps INFO @ Sat, 24 Aug 2019 17:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05_model.r WARNING @ Sat, 24 Aug 2019 17:28:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:28:24: #2 You may need to consider one of the other alternative d(s): 50,227,412,504 WARNING @ Sat, 24 Aug 2019 17:28:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:28:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:28:25: 23000000 INFO @ Sat, 24 Aug 2019 17:28:27: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:28:27: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:28:27: #1 total tags in treatment: 27562800 INFO @ Sat, 24 Aug 2019 17:28:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:28:27: #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 17:28:28: #1 tags after filtering in treatment: 27562703 INFO @ Sat, 24 Aug 2019 17:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:28:28: #1 finished! INFO @ Sat, 24 Aug 2019 17:28:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:28:31: #2 number of paired peaks: 6706 INFO @ Sat, 24 Aug 2019 17:28:31: start model_add_line... INFO @ Sat, 24 Aug 2019 17:28:31: start X-correlation... INFO @ Sat, 24 Aug 2019 17:28:31: end of X-cor INFO @ Sat, 24 Aug 2019 17:28:31: #2 finished! INFO @ Sat, 24 Aug 2019 17:28:31: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:28:31: #2 alternative fragment length(s) may be 50,227,412,504 bps INFO @ Sat, 24 Aug 2019 17:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10_model.r WARNING @ Sat, 24 Aug 2019 17:28:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:28:31: #2 You may need to consider one of the other alternative d(s): 50,227,412,504 WARNING @ Sat, 24 Aug 2019 17:28:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:28:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:28:32: 24000000 INFO @ Sat, 24 Aug 2019 17:28:39: 25000000 INFO @ Sat, 24 Aug 2019 17:28:46: 26000000 INFO @ Sat, 24 Aug 2019 17:28:53: 27000000 INFO @ Sat, 24 Aug 2019 17:28:57: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:28:57: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:28:57: #1 total tags in treatment: 27562800 INFO @ Sat, 24 Aug 2019 17:28:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:28:57: #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 17:28:58: #1 tags after filtering in treatment: 27562703 INFO @ Sat, 24 Aug 2019 17:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:28:58: #1 finished! INFO @ Sat, 24 Aug 2019 17:28:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:29:01: #2 number of paired peaks: 6706 INFO @ Sat, 24 Aug 2019 17:29:01: start model_add_line... INFO @ Sat, 24 Aug 2019 17:29:02: start X-correlation... INFO @ Sat, 24 Aug 2019 17:29:02: end of X-cor INFO @ Sat, 24 Aug 2019 17:29:02: #2 finished! INFO @ Sat, 24 Aug 2019 17:29:02: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:29:02: #2 alternative fragment length(s) may be 50,227,412,504 bps INFO @ Sat, 24 Aug 2019 17:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20_model.r WARNING @ Sat, 24 Aug 2019 17:29:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:29:02: #2 You may need to consider one of the other alternative d(s): 50,227,412,504 WARNING @ Sat, 24 Aug 2019 17:29:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:29:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:29:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:29:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:29:56: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:30:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.05_summits.bed INFO @ Sat, 24 Aug 2019 17:30:33: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (5684 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.10_summits.bed INFO @ Sat, 24 Aug 2019 17:30:39: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (2863 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337079/ERX337079.20_summits.bed INFO @ Sat, 24 Aug 2019 17:31:10: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1081 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。