Job ID = 1298275 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:41:01 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 ) 2019-06-03T08:41:26 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 ) 2019-06-03T08:44:36 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 ) 2019-06-03T08:44:36 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 ) 2019-06-03T08:45:42 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 ) 2019-06-03T08:47:08 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 ) 2019-06-03T08:49:04 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 ) 2019-06-03T08:50:09 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 ) 2019-06-03T08:50:56 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 ) 2019-06-03T08:56:29 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 ) 2019-06-03T09:05:13 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 ) 2019-06-03T09:08:15 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 ) 2019-06-03T09:09:37 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 ) 2019-06-03T09:11:54 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 ) 2019-06-03T09:13:42 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 : 67,402,205 reads read : 134,804,410 reads written : 134,804,410 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: 00:18:39 67402205 reads; of these: 67402205 (100.00%) were paired; of these: 66659415 (98.90%) aligned concordantly 0 times 589659 (0.87%) aligned concordantly exactly 1 time 153131 (0.23%) aligned concordantly >1 times ---- 66659415 pairs aligned concordantly 0 times; of these: 1633 (0.00%) aligned discordantly 1 time ---- 66657782 pairs aligned 0 times concordantly or discordantly; of these: 133315564 mates make up the pairs; of these: 132657486 (99.51%) aligned 0 times 177079 (0.13%) aligned exactly 1 time 480999 (0.36%) aligned >1 times 1.59% overall alignment rate Time searching: 00:18:39 Overall time: 00:18:39 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] 23079 / 717298 = 0.0322 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 18:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.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 18:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.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 18:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.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 18:40:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:40:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:40:38: 1000000 INFO @ Mon, 03 Jun 2019 18:40:38: 1000000 INFO @ Mon, 03 Jun 2019 18:40:38: 1000000 INFO @ Mon, 03 Jun 2019 18:40:46: 2000000 INFO @ Mon, 03 Jun 2019 18:40:46: 2000000 INFO @ Mon, 03 Jun 2019 18:40:46: 2000000 INFO @ Mon, 03 Jun 2019 18:40:47: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:40:47: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:40:47: #1 total tags in treatment: 719724 INFO @ Mon, 03 Jun 2019 18:40:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:40:47: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:40:47: #1 total tags in treatment: 719724 INFO @ Mon, 03 Jun 2019 18:40:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #1 tags after filtering in treatment: 701140 INFO @ Mon, 03 Jun 2019 18:40:47: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:40:47: #1 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #1 tags after filtering in treatment: 701140 INFO @ Mon, 03 Jun 2019 18:40:47: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:40:47: #1 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:40:47: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:40:47: #1 total tags in treatment: 719724 INFO @ Mon, 03 Jun 2019 18:40:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #1 tags after filtering in treatment: 701140 INFO @ Mon, 03 Jun 2019 18:40:47: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:40:47: #1 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #2 number of paired peaks: 1707 INFO @ Mon, 03 Jun 2019 18:40:47: start model_add_line... INFO @ Mon, 03 Jun 2019 18:40:47: #2 number of paired peaks: 1707 INFO @ Mon, 03 Jun 2019 18:40:47: start model_add_line... INFO @ Mon, 03 Jun 2019 18:40:47: start X-correlation... INFO @ Mon, 03 Jun 2019 18:40:47: start X-correlation... INFO @ Mon, 03 Jun 2019 18:40:47: end of X-cor INFO @ Mon, 03 Jun 2019 18:40:47: #2 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20_model.r INFO @ Mon, 03 Jun 2019 18:40:47: end of X-cor INFO @ Mon, 03 Jun 2019 18:40:47: #2 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05_model.r WARNING @ Mon, 03 Jun 2019 18:40:47: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:40:47: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 18:40:47: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:40:47: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:40:47: #2 number of paired peaks: 1707 INFO @ Mon, 03 Jun 2019 18:40:47: start model_add_line... INFO @ Mon, 03 Jun 2019 18:40:47: start X-correlation... INFO @ Mon, 03 Jun 2019 18:40:47: end of X-cor INFO @ Mon, 03 Jun 2019 18:40:47: #2 finished! INFO @ Mon, 03 Jun 2019 18:40:47: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 18:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10_model.r WARNING @ Mon, 03 Jun 2019 18:40:47: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:40:47: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 18:40:47: #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 18:40:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:40:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:40:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:40:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.20_summits.bed INFO @ Mon, 03 Jun 2019 18:40:51: Done! INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.05_summits.bed INFO @ Mon, 03 Jun 2019 18:40:51: Done! INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10_peaks.xls pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650898/SRX4650898.10_summits.bed INFO @ Mon, 03 Jun 2019 18:40:51: Done! CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (158 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。