Job ID = 1298037 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:13:01 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 ) 2019-06-03T08:14:32 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 ) 2019-06-03T08:14:32 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 ) 2019-06-03T08:14:32 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 ) 2019-06-03T08:15:57 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 : 33,942,787 reads read : 67,885,574 reads written : 67,885,574 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: 00:08:26 33942787 reads; of these: 33942787 (100.00%) were paired; of these: 32550643 (95.90%) aligned concordantly 0 times 1080202 (3.18%) aligned concordantly exactly 1 time 311942 (0.92%) aligned concordantly >1 times ---- 32550643 pairs aligned concordantly 0 times; of these: 3589 (0.01%) aligned discordantly 1 time ---- 32547054 pairs aligned 0 times concordantly or discordantly; of these: 65094108 mates make up the pairs; of these: 64357981 (98.87%) aligned 0 times 208799 (0.32%) aligned exactly 1 time 527328 (0.81%) aligned >1 times 5.20% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 55673 / 1392994 = 0.0400 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 17:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.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 17:34:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:34:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.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 17:34:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:34:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.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 17:34:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:34:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:35:02: 1000000 INFO @ Mon, 03 Jun 2019 17:35:02: 1000000 INFO @ Mon, 03 Jun 2019 17:35:02: 1000000 INFO @ Mon, 03 Jun 2019 17:35:09: 2000000 INFO @ Mon, 03 Jun 2019 17:35:10: 2000000 INFO @ Mon, 03 Jun 2019 17:35:11: 2000000 INFO @ Mon, 03 Jun 2019 17:35:16: 3000000 INFO @ Mon, 03 Jun 2019 17:35:17: 3000000 INFO @ Mon, 03 Jun 2019 17:35:19: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:35:19: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:35:19: #1 total tags in treatment: 1336568 INFO @ Mon, 03 Jun 2019 17:35:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:35:19: #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 17:35:19: #1 tags after filtering in treatment: 1298661 INFO @ Mon, 03 Jun 2019 17:35:19: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:35:19: #1 finished! INFO @ Mon, 03 Jun 2019 17:35:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:35:19: 3000000 INFO @ Mon, 03 Jun 2019 17:35:19: #2 number of paired peaks: 1973 INFO @ Mon, 03 Jun 2019 17:35:19: start model_add_line... INFO @ Mon, 03 Jun 2019 17:35:19: start X-correlation... INFO @ Mon, 03 Jun 2019 17:35:19: end of X-cor INFO @ Mon, 03 Jun 2019 17:35:19: #2 finished! INFO @ Mon, 03 Jun 2019 17:35:19: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 17:35:19: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 17:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20_model.r INFO @ Mon, 03 Jun 2019 17:35:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:35:19: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:35:19: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:35:19: #1 total tags in treatment: 1336568 INFO @ Mon, 03 Jun 2019 17:35:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:35:19: #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 17:35:19: #1 tags after filtering in treatment: 1298661 INFO @ Mon, 03 Jun 2019 17:35:19: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:35:19: #1 finished! INFO @ Mon, 03 Jun 2019 17:35:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:35:20: #2 number of paired peaks: 1973 INFO @ Mon, 03 Jun 2019 17:35:20: start model_add_line... INFO @ Mon, 03 Jun 2019 17:35:20: start X-correlation... INFO @ Mon, 03 Jun 2019 17:35:20: end of X-cor INFO @ Mon, 03 Jun 2019 17:35:20: #2 finished! INFO @ Mon, 03 Jun 2019 17:35:20: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 17:35:20: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 17:35:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05_model.r INFO @ Mon, 03 Jun 2019 17:35:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:35:22: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:35:22: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:35:22: #1 total tags in treatment: 1336568 INFO @ Mon, 03 Jun 2019 17:35:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:35:22: #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 17:35:22: #1 tags after filtering in treatment: 1298661 INFO @ Mon, 03 Jun 2019 17:35:22: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:35:22: #1 finished! INFO @ Mon, 03 Jun 2019 17:35:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:35:22: #2 number of paired peaks: 1973 INFO @ Mon, 03 Jun 2019 17:35:22: start model_add_line... INFO @ Mon, 03 Jun 2019 17:35:22: start X-correlation... INFO @ Mon, 03 Jun 2019 17:35:22: end of X-cor INFO @ Mon, 03 Jun 2019 17:35:22: #2 finished! INFO @ Mon, 03 Jun 2019 17:35:22: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 17:35:22: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 17:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10_model.r INFO @ Mon, 03 Jun 2019 17:35:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:35:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:35:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:35:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:35:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.20_summits.bed INFO @ Mon, 03 Jun 2019 17:35:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.05_summits.bed INFO @ Mon, 03 Jun 2019 17:35:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:35:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650881/SRX4650881.10_summits.bed INFO @ Mon, 03 Jun 2019 17:35:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。