Job ID = 10609059 sra ファイルのダウンロード中... Completed: 201392K bytes transferred in 5 seconds (303758K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... 2018-05-03T22:03:24 fastq-dump.2.9.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2018-05-03T22:03:24 fastq-dump.2.9.0 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.20.0.25' 2018-05-03T22:03:24 fastq-dump.2.9.0 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 '172.20.0.25' 2018-05-03T22:03:24 fastq-dump.2.9.0 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/refseq/BX284605.4' 2018-05-03T22:03:24 fastq-dump.2.9.0 err: data corrupt while selecting function within transform module - failed /home/okishinya/chipatlas/results/ce10/SRX2202786/SRR4319292.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.xml'. If the problem persists, you may consider sending the file to 'sra@ncbi.nlm.nih.gov' for assistance. ============================================================= rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:59 12349440 reads; of these: 12349440 (100.00%) were unpaired; of these: 14085 (0.11%) aligned 0 times 8774973 (71.06%) aligned exactly 1 time 3560382 (28.83%) aligned >1 times 99.89% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2901990 / 12335355 = 0.2353 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, 04 May 2018 07:09:18: # Command line: callpeak -t SRX2202786.bam -f BAM -g ce -n SRX2202786.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202786.05 # format = BAM # ChIP-seq file = ['SRX2202786.bam'] # control file = None # effective genome size = 9.00e+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, 04 May 2018 07:09:18: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:18: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:18: # Command line: callpeak -t SRX2202786.bam -f BAM -g ce -n SRX2202786.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202786.20 # format = BAM # ChIP-seq file = ['SRX2202786.bam'] # control file = None # effective genome size = 9.00e+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, 04 May 2018 07:09:18: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:18: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:18: # Command line: callpeak -t SRX2202786.bam -f BAM -g ce -n SRX2202786.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202786.10 # format = BAM # ChIP-seq file = ['SRX2202786.bam'] # control file = None # effective genome size = 9.00e+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, 04 May 2018 07:09:18: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:18: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:24: 1000000 INFO @ Fri, 04 May 2018 07:09:24: 1000000 INFO @ Fri, 04 May 2018 07:09:24: 1000000 INFO @ Fri, 04 May 2018 07:09:30: 2000000 INFO @ Fri, 04 May 2018 07:09:30: 2000000 INFO @ Fri, 04 May 2018 07:09:30: 2000000 INFO @ Fri, 04 May 2018 07:09:36: 3000000 INFO @ Fri, 04 May 2018 07:09:36: 3000000 INFO @ Fri, 04 May 2018 07:09:36: 3000000 INFO @ Fri, 04 May 2018 07:09:42: 4000000 INFO @ Fri, 04 May 2018 07:09:42: 4000000 INFO @ Fri, 04 May 2018 07:09:43: 4000000 INFO @ Fri, 04 May 2018 07:09:48: 5000000 INFO @ Fri, 04 May 2018 07:09:49: 5000000 INFO @ Fri, 04 May 2018 07:09:49: 5000000 INFO @ Fri, 04 May 2018 07:09:55: 6000000 INFO @ Fri, 04 May 2018 07:09:55: 6000000 INFO @ Fri, 04 May 2018 07:09:55: 6000000 INFO @ Fri, 04 May 2018 07:10:01: 7000000 INFO @ Fri, 04 May 2018 07:10:01: 7000000 INFO @ Fri, 04 May 2018 07:10:01: 7000000 INFO @ Fri, 04 May 2018 07:10:07: 8000000 INFO @ Fri, 04 May 2018 07:10:07: 8000000 INFO @ Fri, 04 May 2018 07:10:08: 8000000 INFO @ Fri, 04 May 2018 07:10:13: 9000000 INFO @ Fri, 04 May 2018 07:10:13: 9000000 INFO @ Fri, 04 May 2018 07:10:14: 9000000 INFO @ Fri, 04 May 2018 07:10:16: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:10:16: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:10:16: #1 total tags in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:16: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:16: #1 tags after filtering in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:16: #1 finished! INFO @ Fri, 04 May 2018 07:10:16: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:16: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:10:16: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:10:16: #1 total tags in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:16: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:16: #1 tags after filtering in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:16: #1 finished! INFO @ Fri, 04 May 2018 07:10:16: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:17: #2 number of paired peaks: 3710 INFO @ Fri, 04 May 2018 07:10:17: start model_add_line... INFO @ Fri, 04 May 2018 07:10:17: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:10:17: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:10:17: #1 total tags in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:17: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:17: start X-correlation... INFO @ Fri, 04 May 2018 07:10:17: end of X-cor INFO @ Fri, 04 May 2018 07:10:17: #2 finished! INFO @ Fri, 04 May 2018 07:10:17: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:10:17: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 04 May 2018 07:10:17: #2.2 Generate R script for model : SRX2202786.05_model.r INFO @ Fri, 04 May 2018 07:10:17: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:10:17: #1 tags after filtering in treatment: 9433365 INFO @ Fri, 04 May 2018 07:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:17: #1 finished! INFO @ Fri, 04 May 2018 07:10:17: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:17: #2 number of paired peaks: 3710 INFO @ Fri, 04 May 2018 07:10:17: start model_add_line... INFO @ Fri, 04 May 2018 07:10:18: start X-correlation... INFO @ Fri, 04 May 2018 07:10:18: end of X-cor INFO @ Fri, 04 May 2018 07:10:18: #2 finished! INFO @ Fri, 04 May 2018 07:10:18: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:10:18: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 04 May 2018 07:10:18: #2.2 Generate R script for model : SRX2202786.20_model.r INFO @ Fri, 04 May 2018 07:10:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:10:18: #2 number of paired peaks: 3710 INFO @ Fri, 04 May 2018 07:10:18: start model_add_line... INFO @ Fri, 04 May 2018 07:10:18: start X-correlation... INFO @ Fri, 04 May 2018 07:10:18: end of X-cor INFO @ Fri, 04 May 2018 07:10:18: #2 finished! INFO @ Fri, 04 May 2018 07:10:18: #2 predicted fragment length is 141 bps INFO @ Fri, 04 May 2018 07:10:18: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 04 May 2018 07:10:18: #2.2 Generate R script for model : SRX2202786.10_model.r INFO @ Fri, 04 May 2018 07:10:18: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:10:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:10:46: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:10:46: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:10:58: #4 Write output xls file... SRX2202786.05_peaks.xls INFO @ Fri, 04 May 2018 07:10:58: #4 Write peak in narrowPeak format file... SRX2202786.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:10:58: #4 Write summits bed file... SRX2202786.05_summits.bed INFO @ Fri, 04 May 2018 07:10:58: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6537 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:10:59: #4 Write output xls file... SRX2202786.20_peaks.xls INFO @ Fri, 04 May 2018 07:10:59: #4 Write peak in narrowPeak format file... SRX2202786.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:10:59: #4 Write summits bed file... SRX2202786.20_summits.bed INFO @ Fri, 04 May 2018 07:10:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1625 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:11:00: #4 Write output xls file... SRX2202786.10_peaks.xls INFO @ Fri, 04 May 2018 07:11:00: #4 Write peak in narrowPeak format file... SRX2202786.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:00: #4 Write summits bed file... SRX2202786.10_summits.bed INFO @ Fri, 04 May 2018 07:11:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3590 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。