Job ID = 1298181 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:08:20 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 : NET - Reading information from the socket failed ) 2019-06-03T08:08:20 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 : NET - Reading information from the socket failed ) 2019-06-03T08:11:44 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 ) 2019-06-03T08:11:44 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 ) 2019-06-03T08:12:50 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 ) 2019-06-03T08:13:06 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 ) 2019-06-03T08:13:06 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 ) 2019-06-03T08:13:06 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 ) 2019-06-03T08:14:14 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 : 13,491,319 reads read : 26,982,638 reads written : 26,982,638 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: 00:03:17 13491319 reads; of these: 13491319 (100.00%) were paired; of these: 13132356 (97.34%) aligned concordantly 0 times 266662 (1.98%) aligned concordantly exactly 1 time 92301 (0.68%) aligned concordantly >1 times ---- 13132356 pairs aligned concordantly 0 times; of these: 1411 (0.01%) aligned discordantly 1 time ---- 13130945 pairs aligned 0 times concordantly or discordantly; of these: 26261890 mates make up the pairs; of these: 25923699 (98.71%) aligned 0 times 103701 (0.39%) aligned exactly 1 time 234490 (0.89%) aligned >1 times 3.92% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 8738 / 359448 = 0.0243 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 17:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.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 17:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.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 17:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.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 17:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:21:03: 1000000 INFO @ Mon, 03 Jun 2019 17:21:03: 1000000 INFO @ Mon, 03 Jun 2019 17:21:03: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:21:03: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:21:03: #1 total tags in treatment: 350232 INFO @ Mon, 03 Jun 2019 17:21:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:21:03: #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 17:21:03: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:21:03: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:21:03: #1 total tags in treatment: 350232 INFO @ Mon, 03 Jun 2019 17:21:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:21:03: #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 17:21:03: #1 tags after filtering in treatment: 346976 INFO @ Mon, 03 Jun 2019 17:21:03: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 17:21:03: #1 finished! INFO @ Mon, 03 Jun 2019 17:21:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:21:03: #1 tags after filtering in treatment: 346976 INFO @ Mon, 03 Jun 2019 17:21:03: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 17:21:03: #1 finished! INFO @ Mon, 03 Jun 2019 17:21:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:21:03: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 17:21:03: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 17:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 17:21:03: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 17:21:03: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 17:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 17:21:03: start X-correlation... INFO @ Mon, 03 Jun 2019 17:21:03: start X-correlation... INFO @ Mon, 03 Jun 2019 17:21:03: end of X-cor INFO @ Mon, 03 Jun 2019 17:21:03: end of X-cor INFO @ Mon, 03 Jun 2019 17:21:03: #2 finished! INFO @ Mon, 03 Jun 2019 17:21:03: #2 finished! INFO @ Mon, 03 Jun 2019 17:21:03: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 17:21:03: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 17:21:03: #2 alternative fragment length(s) may be 96,584 bps INFO @ Mon, 03 Jun 2019 17:21:03: #2 alternative fragment length(s) may be 96,584 bps INFO @ Mon, 03 Jun 2019 17:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10_model.r INFO @ Mon, 03 Jun 2019 17:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05_model.r INFO @ Mon, 03 Jun 2019 17:21:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:21:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:21:04: 1000000 INFO @ Mon, 03 Jun 2019 17:21:05: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:21:05: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:21:05: #1 total tags in treatment: 350232 INFO @ Mon, 03 Jun 2019 17:21:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:21:05: #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 17:21:05: #1 tags after filtering in treatment: 346976 INFO @ Mon, 03 Jun 2019 17:21:05: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 03 Jun 2019 17:21:05: #1 finished! INFO @ Mon, 03 Jun 2019 17:21:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:21:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:21:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:21:05: #2 number of paired peaks: 883 WARNING @ Mon, 03 Jun 2019 17:21:05: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Mon, 03 Jun 2019 17:21:05: start model_add_line... INFO @ Mon, 03 Jun 2019 17:21:05: start X-correlation... INFO @ Mon, 03 Jun 2019 17:21:05: end of X-cor INFO @ Mon, 03 Jun 2019 17:21:05: #2 finished! INFO @ Mon, 03 Jun 2019 17:21:05: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 17:21:05: #2 alternative fragment length(s) may be 96,584 bps INFO @ Mon, 03 Jun 2019 17:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20_model.r INFO @ Mon, 03 Jun 2019 17:21:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.05_summits.bed INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:21:05: Done! INFO @ Mon, 03 Jun 2019 17:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.10_summits.bed INFO @ Mon, 03 Jun 2019 17:21:05: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 millis pass2 - checking and writing primary data (41 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:21:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650891/SRX4650891.20_summits.bed INFO @ Mon, 03 Jun 2019 17:21:06: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。