Job ID = 1303768 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:28:38 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 ) 2019-06-03T11:28:38 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 ) 2019-06-03T11:28:38 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 ) 2019-06-03T11:31:27 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 ) 2019-06-03T11:34:51 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 : 11,752,637 reads read : 23,505,274 reads written : 11,752,637 reads 0-length : 11,752,637 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:31 11752637 reads; of these: 11752637 (100.00%) were unpaired; of these: 4273008 (36.36%) aligned 0 times 2631304 (22.39%) aligned exactly 1 time 4848325 (41.25%) aligned >1 times 63.64% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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_rmdupse_core] 4336159 / 7479629 = 0.5797 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 20:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.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 20:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.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 20:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.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 20:47:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:47:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:48:06: 1000000 INFO @ Mon, 03 Jun 2019 20:48:10: 1000000 INFO @ Mon, 03 Jun 2019 20:48:11: 1000000 INFO @ Mon, 03 Jun 2019 20:48:16: 2000000 INFO @ Mon, 03 Jun 2019 20:48:25: 2000000 INFO @ Mon, 03 Jun 2019 20:48:26: 2000000 INFO @ Mon, 03 Jun 2019 20:48:27: 3000000 INFO @ Mon, 03 Jun 2019 20:48:28: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:48:28: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:48:28: #1 total tags in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:28: #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 20:48:28: #1 tags after filtering in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:48:28: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:28: #2 number of paired peaks: 1854 INFO @ Mon, 03 Jun 2019 20:48:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:48:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:48:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:48:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:48:28: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 20:48:28: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 20:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10_model.r WARNING @ Mon, 03 Jun 2019 20:48:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:48:28: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 20:48:28: #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 20:48:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:48:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:48:38: 3000000 INFO @ Mon, 03 Jun 2019 20:48:40: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:48:40: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:48:40: #1 total tags in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:40: #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 20:48:40: #1 tags after filtering in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:48:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:41: 3000000 INFO @ Mon, 03 Jun 2019 20:48:41: #2 number of paired peaks: 1854 INFO @ Mon, 03 Jun 2019 20:48:41: start model_add_line... INFO @ Mon, 03 Jun 2019 20:48:41: start X-correlation... INFO @ Mon, 03 Jun 2019 20:48:41: end of X-cor INFO @ Mon, 03 Jun 2019 20:48:41: #2 finished! INFO @ Mon, 03 Jun 2019 20:48:41: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 20:48:41: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 20:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20_model.r WARNING @ Mon, 03 Jun 2019 20:48:41: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:48:41: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 20:48:41: #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 20:48:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:48:42: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 20:48:42: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 20:48:42: #1 total tags in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:42: #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 20:48:42: #1 tags after filtering in treatment: 3143470 INFO @ Mon, 03 Jun 2019 20:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:48:42: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:43: #2 number of paired peaks: 1854 INFO @ Mon, 03 Jun 2019 20:48:43: start model_add_line... INFO @ Mon, 03 Jun 2019 20:48:43: start X-correlation... INFO @ Mon, 03 Jun 2019 20:48:43: end of X-cor INFO @ Mon, 03 Jun 2019 20:48:43: #2 finished! INFO @ Mon, 03 Jun 2019 20:48:43: #2 predicted fragment length is 73 bps INFO @ Mon, 03 Jun 2019 20:48:43: #2 alternative fragment length(s) may be 73 bps INFO @ Mon, 03 Jun 2019 20:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05_model.r WARNING @ Mon, 03 Jun 2019 20:48:43: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:48:43: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Mon, 03 Jun 2019 20:48:43: #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 20:48:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.10_summits.bed INFO @ Mon, 03 Jun 2019 20:48:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1212 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:48:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:48:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.20_summits.bed INFO @ Mon, 03 Jun 2019 20:48:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 20:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941152/SRX4941152.05_summits.bed INFO @ Mon, 03 Jun 2019 20:48:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2139 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。