Job ID = 1293915 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:11:20 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 ) 2019-06-02T18:15:51 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:15:51 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000068.6' 2019-06-02T18:15:56 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:15:56 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000075.5' 2019-06-02T18:16:00 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:16:00 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000075.5' 2019-06-02T18:16:05 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:16:05 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000068.6' 2019-06-02T18:16:15 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #6219777 ).VCursorCellDataDirect() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:16:15 fasterq-dump.2.9.6 err: sorter.c write_to_store().pack_read_2_4na() failed RC(rcVDB,rcNoTarg,rcWriting,rcFormat,rcNull) 2019-06-02T18:16:15 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:16:15 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000081.5' 2019-06-02T18:25:28 fasterq-dump.2.9.6 err: sorter.c run_producer_pool().join_and_release_threads -> RC(rcVDB,rcNoTarg,rcWriting,rcFormat,rcNull) 2019-06-02T18:25:28 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcWriting,rcFormat,rcNull) 2019-06-02T18:25:28 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcWriting,rcFormat,rcNull) 2019-06-02T18:26:13 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:26:13 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR2984038/SRR2984038.1' 2019-06-02T18:26:13 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR2984038' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T18:26:13 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 0 of 59513338 2019-06-02T18:26:13 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-06-02T18:26:13 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) spots read : 69,969,043 reads read : 69,969,043 reads written : 69,969,043 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: 00:08:48 69969043 reads; of these: 69969043 (100.00%) were unpaired; of these: 67700633 (96.76%) aligned 0 times 1478817 (2.11%) aligned exactly 1 time 789593 (1.13%) aligned >1 times 3.24% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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_rmdupse_core] 480441 / 2268410 = 0.2118 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 03:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.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 03:59:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:59:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.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 03:59:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:59:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.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 03:59:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:59:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:00:00: 1000000 INFO @ Mon, 03 Jun 2019 04:00:00: 1000000 INFO @ Mon, 03 Jun 2019 04:00:01: 1000000 INFO @ Mon, 03 Jun 2019 04:00:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:00:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:00:06: #1 total tags in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:00:06: #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 04:00:06: #1 tags after filtering in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:00:06: #1 finished! INFO @ Mon, 03 Jun 2019 04:00:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:00:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:00:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:00:06: #1 total tags in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:00:06: #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 04:00:06: #1 tags after filtering in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:00:06: #1 finished! INFO @ Mon, 03 Jun 2019 04:00:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:00:06: #2 number of paired peaks: 4430 INFO @ Mon, 03 Jun 2019 04:00:06: start model_add_line... INFO @ Mon, 03 Jun 2019 04:00:06: start X-correlation... INFO @ Mon, 03 Jun 2019 04:00:06: end of X-cor INFO @ Mon, 03 Jun 2019 04:00:06: #2 finished! INFO @ Mon, 03 Jun 2019 04:00:06: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 04:00:06: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 04:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20_model.r WARNING @ Mon, 03 Jun 2019 04:00:06: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:00:06: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 04:00:06: #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 04:00:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:00:06: #2 number of paired peaks: 4430 INFO @ Mon, 03 Jun 2019 04:00:06: start model_add_line... INFO @ Mon, 03 Jun 2019 04:00:06: start X-correlation... INFO @ Mon, 03 Jun 2019 04:00:06: end of X-cor INFO @ Mon, 03 Jun 2019 04:00:06: #2 finished! INFO @ Mon, 03 Jun 2019 04:00:06: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 04:00:06: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 04:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10_model.r WARNING @ Mon, 03 Jun 2019 04:00:06: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:00:06: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 04:00:06: #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 04:00:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:00:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:00:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:00:08: #1 total tags in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:00:08: #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 04:00:08: #1 tags after filtering in treatment: 1787969 INFO @ Mon, 03 Jun 2019 04:00:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:00:08: #1 finished! INFO @ Mon, 03 Jun 2019 04:00:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:00:08: #2 number of paired peaks: 4430 INFO @ Mon, 03 Jun 2019 04:00:08: start model_add_line... INFO @ Mon, 03 Jun 2019 04:00:08: start X-correlation... INFO @ Mon, 03 Jun 2019 04:00:08: end of X-cor INFO @ Mon, 03 Jun 2019 04:00:08: #2 finished! INFO @ Mon, 03 Jun 2019 04:00:08: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 04:00:08: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 04:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05_model.r WARNING @ Mon, 03 Jun 2019 04:00:08: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:00:08: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 04:00:08: #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 04:00:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:00:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:00:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:00:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.20_summits.bed INFO @ Mon, 03 Jun 2019 04:00:15: Done! INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10_peaks.xls pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (202 records, 4 fields): 2 millis INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.10_summits.bed CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:00:15: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473019/SRX1473019.05_summits.bed INFO @ Mon, 03 Jun 2019 04:00:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1768 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。