Job ID = 1294471 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:10:23 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' 2019-06-02T23:10:23 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/sra12/SRR/000849/SRR869860' 2019-06-02T23:10:23 fasterq-dump.2.9.6 err: invalid accession 'SRR869860' 2019-06-02T23:16:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T23:16:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 1900-01-00T00:00:00 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,272,941 reads read : 14,272,941 reads written : 14,272,941 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:48 14272941 reads; of these: 14272941 (100.00%) were unpaired; of these: 698546 (4.89%) aligned 0 times 2252361 (15.78%) aligned exactly 1 time 11322034 (79.33%) aligned >1 times 95.11% overall alignment rate Time searching: 00:14:49 Overall time: 00:14:49 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6058420 / 13574395 = 0.4463 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 08:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.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 08:40:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.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 08:40:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.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 08:40:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:40:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:40:09: 1000000 INFO @ Mon, 03 Jun 2019 08:40:10: 1000000 INFO @ Mon, 03 Jun 2019 08:40:10: 1000000 INFO @ Mon, 03 Jun 2019 08:40:17: 2000000 INFO @ Mon, 03 Jun 2019 08:40:17: 2000000 INFO @ Mon, 03 Jun 2019 08:40:19: 2000000 INFO @ Mon, 03 Jun 2019 08:40:25: 3000000 INFO @ Mon, 03 Jun 2019 08:40:25: 3000000 INFO @ Mon, 03 Jun 2019 08:40:28: 3000000 INFO @ Mon, 03 Jun 2019 08:40:32: 4000000 INFO @ Mon, 03 Jun 2019 08:40:33: 4000000 INFO @ Mon, 03 Jun 2019 08:40:37: 4000000 INFO @ Mon, 03 Jun 2019 08:40:39: 5000000 INFO @ Mon, 03 Jun 2019 08:40:41: 5000000 INFO @ Mon, 03 Jun 2019 08:40:46: 5000000 INFO @ Mon, 03 Jun 2019 08:40:47: 6000000 INFO @ Mon, 03 Jun 2019 08:40:48: 6000000 INFO @ Mon, 03 Jun 2019 08:40:54: 7000000 INFO @ Mon, 03 Jun 2019 08:40:55: 6000000 INFO @ Mon, 03 Jun 2019 08:40:56: 7000000 INFO @ Mon, 03 Jun 2019 08:40:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:57: #1 total tags in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:40:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:57: #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 08:40:57: #1 tags after filtering in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:57: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:58: #2 number of paired peaks: 2493 INFO @ Mon, 03 Jun 2019 08:40:58: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:58: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:59: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 08:40:59: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 08:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10_model.r WARNING @ Mon, 03 Jun 2019 08:40:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:59: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 08:40:59: #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 08:40:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:41:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:41:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:41:00: #1 total tags in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:41:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:41:00: #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 08:41:00: #1 tags after filtering in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:41:00: #1 finished! INFO @ Mon, 03 Jun 2019 08:41:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:41:01: #2 number of paired peaks: 2493 INFO @ Mon, 03 Jun 2019 08:41:01: start model_add_line... INFO @ Mon, 03 Jun 2019 08:41:01: start X-correlation... INFO @ Mon, 03 Jun 2019 08:41:01: end of X-cor INFO @ Mon, 03 Jun 2019 08:41:01: #2 finished! INFO @ Mon, 03 Jun 2019 08:41:01: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 08:41:01: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 08:41:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05_model.r WARNING @ Mon, 03 Jun 2019 08:41:01: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:41:01: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 08:41:01: #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 08:41:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:41:03: 7000000 INFO @ Mon, 03 Jun 2019 08:41:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:41:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:41:08: #1 total tags in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:41:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:41:08: #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 08:41:08: #1 tags after filtering in treatment: 7515975 INFO @ Mon, 03 Jun 2019 08:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:41:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:41:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:41:09: #2 number of paired peaks: 2493 INFO @ Mon, 03 Jun 2019 08:41:09: start model_add_line... INFO @ Mon, 03 Jun 2019 08:41:09: start X-correlation... INFO @ Mon, 03 Jun 2019 08:41:09: end of X-cor INFO @ Mon, 03 Jun 2019 08:41:09: #2 finished! INFO @ Mon, 03 Jun 2019 08:41:09: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 08:41:09: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 08:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20_model.r WARNING @ Mon, 03 Jun 2019 08:41:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:41:09: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 08:41:09: #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 08:41:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:41:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.10_summits.bed INFO @ Mon, 03 Jun 2019 08:41:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2350 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.05_summits.bed INFO @ Mon, 03 Jun 2019 08:41:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5692 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287672/SRX287672.20_summits.bed INFO @ Mon, 03 Jun 2019 08:41:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。