Job ID = 10609056 sra ファイルのダウンロード中... Completed: 204908K bytes transferred in 24 seconds (68956K 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... 2018-05-03T22:03:23 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 ) 2018-05-03T22:03:23 fastq-dump.2.9.0 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.20.0.2' 2018-05-03T22:03:23 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 '172.20.0.2' 2018-05-03T22:03:23 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' Read 20182598 spots for /home/okishinya/chipatlas/results/ce10/SRX2202783/SRR4319289.sra Written 20182598 spots for /home/okishinya/chipatlas/results/ce10/SRX2202783/SRR4319289.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:12 20182598 reads; of these: 20182598 (100.00%) were unpaired; of these: 1497158 (7.42%) aligned 0 times 11668621 (57.82%) aligned exactly 1 time 7016819 (34.77%) aligned >1 times 92.58% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 6760220 / 18685440 = 0.3618 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 07:12:40: # Command line: callpeak -t SRX2202783.bam -f BAM -g ce -n SRX2202783.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202783.10 # format = BAM # ChIP-seq file = ['SRX2202783.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 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:40: # Command line: callpeak -t SRX2202783.bam -f BAM -g ce -n SRX2202783.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202783.20 # format = BAM # ChIP-seq file = ['SRX2202783.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 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:40: # Command line: callpeak -t SRX2202783.bam -f BAM -g ce -n SRX2202783.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202783.05 # format = BAM # ChIP-seq file = ['SRX2202783.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 07:12:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:47: 1000000 INFO @ Fri, 04 May 2018 07:12:53: 2000000 INFO @ Fri, 04 May 2018 07:12:54: 2000000 INFO @ Fri, 04 May 2018 07:12:54: 2000000 INFO @ Fri, 04 May 2018 07:13:00: 3000000 INFO @ Fri, 04 May 2018 07:13:01: 3000000 INFO @ Fri, 04 May 2018 07:13:01: 3000000 INFO @ Fri, 04 May 2018 07:13:07: 4000000 INFO @ Fri, 04 May 2018 07:13:08: 4000000 INFO @ Fri, 04 May 2018 07:13:08: 4000000 INFO @ Fri, 04 May 2018 07:13:14: 5000000 INFO @ Fri, 04 May 2018 07:13:15: 5000000 INFO @ Fri, 04 May 2018 07:13:15: 5000000 INFO @ Fri, 04 May 2018 07:13:21: 6000000 INFO @ Fri, 04 May 2018 07:13:22: 6000000 INFO @ Fri, 04 May 2018 07:13:22: 6000000 INFO @ Fri, 04 May 2018 07:13:29: 7000000 INFO @ Fri, 04 May 2018 07:13:29: 7000000 INFO @ Fri, 04 May 2018 07:13:29: 7000000 INFO @ Fri, 04 May 2018 07:13:36: 8000000 INFO @ Fri, 04 May 2018 07:13:36: 8000000 INFO @ Fri, 04 May 2018 07:13:36: 8000000 INFO @ Fri, 04 May 2018 07:13:43: 9000000 INFO @ Fri, 04 May 2018 07:13:44: 9000000 INFO @ Fri, 04 May 2018 07:13:44: 9000000 INFO @ Fri, 04 May 2018 07:13:51: 10000000 INFO @ Fri, 04 May 2018 07:13:51: 10000000 INFO @ Fri, 04 May 2018 07:13:52: 10000000 INFO @ Fri, 04 May 2018 07:13:58: 11000000 INFO @ Fri, 04 May 2018 07:13:58: 11000000 INFO @ Fri, 04 May 2018 07:14:00: 11000000 INFO @ Fri, 04 May 2018 07:14:05: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:14:05: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:14:05: #1 total tags in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:05: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:05: #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 07:14:05: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:14:05: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:14:05: #1 total tags in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:05: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:05: #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 07:14:05: #1 tags after filtering in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:05: #1 finished! INFO @ Fri, 04 May 2018 07:14:05: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:06: #1 tags after filtering in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:06: #1 finished! INFO @ Fri, 04 May 2018 07:14:06: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:07: #2 number of paired peaks: 3978 INFO @ Fri, 04 May 2018 07:14:07: start model_add_line... INFO @ Fri, 04 May 2018 07:14:07: #2 number of paired peaks: 3978 INFO @ Fri, 04 May 2018 07:14:07: start model_add_line... INFO @ Fri, 04 May 2018 07:14:07: start X-correlation... INFO @ Fri, 04 May 2018 07:14:07: end of X-cor INFO @ Fri, 04 May 2018 07:14:07: #2 finished! INFO @ Fri, 04 May 2018 07:14:07: #2 predicted fragment length is 137 bps INFO @ Fri, 04 May 2018 07:14:07: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 04 May 2018 07:14:07: #2.2 Generate R script for model : SRX2202783.05_model.r INFO @ Fri, 04 May 2018 07:14:07: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:07: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:14:07: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:14:07: #1 total tags in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:07: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:07: #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 07:14:07: start X-correlation... INFO @ Fri, 04 May 2018 07:14:07: end of X-cor INFO @ Fri, 04 May 2018 07:14:07: #2 finished! INFO @ Fri, 04 May 2018 07:14:07: #2 predicted fragment length is 137 bps INFO @ Fri, 04 May 2018 07:14:07: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 04 May 2018 07:14:07: #2.2 Generate R script for model : SRX2202783.20_model.r INFO @ Fri, 04 May 2018 07:14:07: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:07: #1 tags after filtering in treatment: 11925220 INFO @ Fri, 04 May 2018 07:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:07: #1 finished! INFO @ Fri, 04 May 2018 07:14:07: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:08: #2 number of paired peaks: 3978 INFO @ Fri, 04 May 2018 07:14:08: start model_add_line... INFO @ Fri, 04 May 2018 07:14:09: start X-correlation... INFO @ Fri, 04 May 2018 07:14:09: end of X-cor INFO @ Fri, 04 May 2018 07:14:09: #2 finished! INFO @ Fri, 04 May 2018 07:14:09: #2 predicted fragment length is 137 bps INFO @ Fri, 04 May 2018 07:14:09: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 04 May 2018 07:14:09: #2.2 Generate R script for model : SRX2202783.10_model.r INFO @ Fri, 04 May 2018 07:14:09: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:46: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:59: #4 Write output xls file... SRX2202783.05_peaks.xls INFO @ Fri, 04 May 2018 07:14:59: #4 Write peak in narrowPeak format file... SRX2202783.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:59: #4 Write summits bed file... SRX2202783.05_summits.bed INFO @ Fri, 04 May 2018 07:14:59: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (12091 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:14:59: #4 Write output xls file... SRX2202783.10_peaks.xls INFO @ Fri, 04 May 2018 07:14:59: #4 Write peak in narrowPeak format file... SRX2202783.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:00: #4 Write summits bed file... SRX2202783.10_summits.bed INFO @ Fri, 04 May 2018 07:15:00: Done! pass1 - making usageList (6 chroms): 2 millis INFO @ Fri, 04 May 2018 07:15:00: #4 Write output xls file... SRX2202783.20_peaks.xls pass2 - checking and writing primary data (8814 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:00: #4 Write peak in narrowPeak format file... SRX2202783.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:00: #4 Write summits bed file... SRX2202783.20_summits.bed INFO @ Fri, 04 May 2018 07:15:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5241 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。