Job ID = 1298016 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:04:56 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) : NET - Reading information from the socket failed ) 2019-06-03T08:04:56 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) : NET - Reading information from the socket failed ) 2019-06-03T08:04:56 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) : NET - Reading information from the socket failed ) 2019-06-03T08:18:06 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 ) 2019-06-03T08:18:06 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 ) 2019-06-03T08:18:06 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 ) 2019-06-03T08:20:33 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 ) 2019-06-03T08:20:33 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 : 37,440,054 reads read : 74,880,108 reads written : 74,880,108 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: 00:13:23 37440054 reads; of these: 37440054 (100.00%) were paired; of these: 34094348 (91.06%) aligned concordantly 0 times 2738522 (7.31%) aligned concordantly exactly 1 time 607184 (1.62%) aligned concordantly >1 times ---- 34094348 pairs aligned concordantly 0 times; of these: 30309 (0.09%) aligned discordantly 1 time ---- 34064039 pairs aligned 0 times concordantly or discordantly; of these: 68128078 mates make up the pairs; of these: 66609749 (97.77%) aligned 0 times 810509 (1.19%) aligned exactly 1 time 707820 (1.04%) aligned >1 times 11.04% overall alignment rate Time searching: 00:13:23 Overall time: 00:13:23 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 136976 / 3353731 = 0.0408 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 17:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.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 17:40:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.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 17:40:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.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 17:40:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:40:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:40:45: 1000000 INFO @ Mon, 03 Jun 2019 17:40:45: 1000000 INFO @ Mon, 03 Jun 2019 17:40:45: 1000000 INFO @ Mon, 03 Jun 2019 17:40:53: 2000000 INFO @ Mon, 03 Jun 2019 17:40:53: 2000000 INFO @ Mon, 03 Jun 2019 17:40:53: 2000000 INFO @ Mon, 03 Jun 2019 17:41:01: 3000000 INFO @ Mon, 03 Jun 2019 17:41:02: 3000000 INFO @ Mon, 03 Jun 2019 17:41:02: 3000000 INFO @ Mon, 03 Jun 2019 17:41:09: 4000000 INFO @ Mon, 03 Jun 2019 17:41:10: 4000000 INFO @ Mon, 03 Jun 2019 17:41:10: 4000000 INFO @ Mon, 03 Jun 2019 17:41:17: 5000000 INFO @ Mon, 03 Jun 2019 17:41:18: 5000000 INFO @ Mon, 03 Jun 2019 17:41:18: 5000000 INFO @ Mon, 03 Jun 2019 17:41:25: 6000000 INFO @ Mon, 03 Jun 2019 17:41:26: 6000000 INFO @ Mon, 03 Jun 2019 17:41:26: 6000000 INFO @ Mon, 03 Jun 2019 17:41:33: 7000000 INFO @ Mon, 03 Jun 2019 17:41:34: 7000000 INFO @ Mon, 03 Jun 2019 17:41:34: 7000000 INFO @ Mon, 03 Jun 2019 17:41:40: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:41:40: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:41:40: #1 total tags in treatment: 3208953 INFO @ Mon, 03 Jun 2019 17:41:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:41:40: #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 17:41:40: #1 tags after filtering in treatment: 3033525 INFO @ Mon, 03 Jun 2019 17:41:40: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:41:40: #1 finished! INFO @ Mon, 03 Jun 2019 17:41:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:41:40: #2 number of paired peaks: 1126 INFO @ Mon, 03 Jun 2019 17:41:40: start model_add_line... INFO @ Mon, 03 Jun 2019 17:41:40: start X-correlation... INFO @ Mon, 03 Jun 2019 17:41:40: end of X-cor INFO @ Mon, 03 Jun 2019 17:41:40: #2 finished! INFO @ Mon, 03 Jun 2019 17:41:40: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 17:41:40: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 17:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05_model.r INFO @ Mon, 03 Jun 2019 17:41:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:41:41: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:41:41: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:41:41: #1 total tags in treatment: 3208953 INFO @ Mon, 03 Jun 2019 17:41:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:41:41: #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 17:41:41: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:41:41: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:41:41: #1 total tags in treatment: 3208953 INFO @ Mon, 03 Jun 2019 17:41:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:41:41: #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 17:41:42: #1 tags after filtering in treatment: 3033525 INFO @ Mon, 03 Jun 2019 17:41:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:41:42: #1 finished! INFO @ Mon, 03 Jun 2019 17:41:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:41:42: #1 tags after filtering in treatment: 3033525 INFO @ Mon, 03 Jun 2019 17:41:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:41:42: #1 finished! INFO @ Mon, 03 Jun 2019 17:41:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:41:42: #2 number of paired peaks: 1126 INFO @ Mon, 03 Jun 2019 17:41:42: start model_add_line... INFO @ Mon, 03 Jun 2019 17:41:42: #2 number of paired peaks: 1126 INFO @ Mon, 03 Jun 2019 17:41:42: start model_add_line... INFO @ Mon, 03 Jun 2019 17:41:42: start X-correlation... INFO @ Mon, 03 Jun 2019 17:41:42: end of X-cor INFO @ Mon, 03 Jun 2019 17:41:42: #2 finished! INFO @ Mon, 03 Jun 2019 17:41:42: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 17:41:42: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 17:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10_model.r INFO @ Mon, 03 Jun 2019 17:41:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:41:42: start X-correlation... INFO @ Mon, 03 Jun 2019 17:41:42: end of X-cor INFO @ Mon, 03 Jun 2019 17:41:42: #2 finished! INFO @ Mon, 03 Jun 2019 17:41:42: #2 predicted fragment length is 141 bps INFO @ Mon, 03 Jun 2019 17:41:42: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 03 Jun 2019 17:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20_model.r INFO @ Mon, 03 Jun 2019 17:41:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:41:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:41:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:41:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:41:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:41:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:41:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.05_summits.bed INFO @ Mon, 03 Jun 2019 17:41:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.20_summits.bed INFO @ Mon, 03 Jun 2019 17:41:56: Done! INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10_peaks.xls pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 2 millis INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650878/SRX4650878.10_summits.bed INFO @ Mon, 03 Jun 2019 17:41:56: Done! CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (324 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。