Job ID = 1307166 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:06:40 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 ) 2019-06-03T13:06:40 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 ) 2019-06-03T13:06:40 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 ) 2019-06-03T13:06:40 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 ) 2019-06-03T13:10:56 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 ) 2019-06-03T13:10:56 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 ) spots read : 18,678,944 reads read : 37,357,888 reads written : 18,678,944 reads 0-length : 18,678,944 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: 00:06:42 18678944 reads; of these: 18678944 (100.00%) were unpaired; of these: 437536 (2.34%) aligned 0 times 16898876 (90.47%) aligned exactly 1 time 1342532 (7.19%) aligned >1 times 97.66% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9346847 / 18241408 = 0.5124 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 22:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.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 22:26:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.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 22:26:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.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 22:26:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:26:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:26:51: 1000000 INFO @ Mon, 03 Jun 2019 22:26:51: 1000000 INFO @ Mon, 03 Jun 2019 22:26:51: 1000000 INFO @ Mon, 03 Jun 2019 22:27:00: 2000000 INFO @ Mon, 03 Jun 2019 22:27:00: 2000000 INFO @ Mon, 03 Jun 2019 22:27:01: 2000000 INFO @ Mon, 03 Jun 2019 22:27:10: 3000000 INFO @ Mon, 03 Jun 2019 22:27:10: 3000000 INFO @ Mon, 03 Jun 2019 22:27:10: 3000000 INFO @ Mon, 03 Jun 2019 22:27:19: 4000000 INFO @ Mon, 03 Jun 2019 22:27:19: 4000000 INFO @ Mon, 03 Jun 2019 22:27:19: 4000000 INFO @ Mon, 03 Jun 2019 22:27:28: 5000000 INFO @ Mon, 03 Jun 2019 22:27:28: 5000000 INFO @ Mon, 03 Jun 2019 22:27:28: 5000000 INFO @ Mon, 03 Jun 2019 22:27:37: 6000000 INFO @ Mon, 03 Jun 2019 22:27:37: 6000000 INFO @ Mon, 03 Jun 2019 22:27:38: 6000000 INFO @ Mon, 03 Jun 2019 22:27:46: 7000000 INFO @ Mon, 03 Jun 2019 22:27:47: 7000000 INFO @ Mon, 03 Jun 2019 22:27:47: 7000000 INFO @ Mon, 03 Jun 2019 22:27:56: 8000000 INFO @ Mon, 03 Jun 2019 22:27:56: 8000000 INFO @ Mon, 03 Jun 2019 22:27:56: 8000000 INFO @ Mon, 03 Jun 2019 22:28:04: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:28:04: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:28:04: #1 total tags in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:04: #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 22:28:04: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:28:04: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:28:04: #1 total tags in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:04: #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 22:28:04: #1 tags after filtering in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:04: #1 tags after filtering in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:04: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:28:04: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:28:04: #1 total tags in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:28:04: #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 22:28:04: #1 tags after filtering in treatment: 8894561 INFO @ Mon, 03 Jun 2019 22:28:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:28:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:28:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:28:06: #2 number of paired peaks: 12760 INFO @ Mon, 03 Jun 2019 22:28:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:06: #2 number of paired peaks: 12760 INFO @ Mon, 03 Jun 2019 22:28:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:06: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:06: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 22:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20_model.r WARNING @ Mon, 03 Jun 2019 22:28:06: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:28:06: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Mon, 03 Jun 2019 22:28:06: #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 22:28:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:28:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:06: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:06: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 22:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10_model.r WARNING @ Mon, 03 Jun 2019 22:28:06: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:28:06: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Mon, 03 Jun 2019 22:28:06: #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 22:28:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:28:06: #2 number of paired peaks: 12760 INFO @ Mon, 03 Jun 2019 22:28:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:28:07: start X-correlation... INFO @ Mon, 03 Jun 2019 22:28:07: end of X-cor INFO @ Mon, 03 Jun 2019 22:28:07: #2 finished! INFO @ Mon, 03 Jun 2019 22:28:07: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 22:28:07: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 22:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05_model.r WARNING @ Mon, 03 Jun 2019 22:28:07: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:28:07: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Mon, 03 Jun 2019 22:28:07: #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 22:28:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:28:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 22:28:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:28:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.20_summits.bed INFO @ Mon, 03 Jun 2019 22:28:45: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7713 records, 4 fields): 16 millis INFO @ Mon, 03 Jun 2019 22:28:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.10_summits.bed INFO @ Mon, 03 Jun 2019 22:28:46: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8667 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241028/SRX5241028.05_summits.bed INFO @ Mon, 03 Jun 2019 22:28:47: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9311 records, 4 fields): 16 millis CompletedMACS2peakCalling