Job ID = 1301150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:35:39 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 ) 2019-06-03T10:35:39 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 ) 2019-06-03T10:35:39 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 ) 2019-06-03T10:37:00 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 ) 2019-06-03T10:37:00 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 ) 2019-06-03T10:37:04 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 ) spots read : 32,907,349 reads read : 32,907,349 reads written : 32,907,349 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: 00:15:10 32907349 reads; of these: 32907349 (100.00%) were unpaired; of these: 20609714 (62.63%) aligned 0 times 10592299 (32.19%) aligned exactly 1 time 1705336 (5.18%) aligned >1 times 37.37% overall alignment rate Time searching: 00:15:10 Overall time: 00:15:10 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] 9100115 / 12297635 = 0.7400 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 20:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.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 20:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.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 20:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.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 20:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:31:08: 1000000 INFO @ Mon, 03 Jun 2019 20:31:09: 1000000 INFO @ Mon, 03 Jun 2019 20:31:11: 1000000 INFO @ Mon, 03 Jun 2019 20:31:23: 2000000 INFO @ Mon, 03 Jun 2019 20:31:25: 2000000 INFO @ Mon, 03 Jun 2019 20:31:29: 2000000 INFO @ Mon, 03 Jun 2019 20:31:37: 3000000 INFO @ Mon, 03 Jun 2019 20:31:40: #1 tag size is determined as 101 bps INFO @ Mon, 03 Jun 2019 20:31:40: #1 tag size = 101 INFO @ Mon, 03 Jun 2019 20:31:40: #1 total tags in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:31:40: #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 20:31:40: #1 tags after filtering in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:31:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:31:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:31:40: #2 number of paired peaks: 3917 INFO @ Mon, 03 Jun 2019 20:31:40: start model_add_line... INFO @ Mon, 03 Jun 2019 20:31:40: start X-correlation... INFO @ Mon, 03 Jun 2019 20:31:40: end of X-cor INFO @ Mon, 03 Jun 2019 20:31:40: #2 finished! INFO @ Mon, 03 Jun 2019 20:31:40: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 20:31:40: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 20:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10_model.r WARNING @ Mon, 03 Jun 2019 20:31:40: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:31:40: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 20:31:40: #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 20:31:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:31:42: 3000000 INFO @ Mon, 03 Jun 2019 20:31:45: #1 tag size is determined as 101 bps INFO @ Mon, 03 Jun 2019 20:31:45: #1 tag size = 101 INFO @ Mon, 03 Jun 2019 20:31:45: #1 total tags in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:31:45: #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 20:31:45: #1 tags after filtering in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:31:45: #1 finished! INFO @ Mon, 03 Jun 2019 20:31:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:31:45: 3000000 INFO @ Mon, 03 Jun 2019 20:31:46: #2 number of paired peaks: 3917 INFO @ Mon, 03 Jun 2019 20:31:46: start model_add_line... INFO @ Mon, 03 Jun 2019 20:31:46: start X-correlation... INFO @ Mon, 03 Jun 2019 20:31:46: end of X-cor INFO @ Mon, 03 Jun 2019 20:31:46: #2 finished! INFO @ Mon, 03 Jun 2019 20:31:46: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 20:31:46: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 20:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20_model.r WARNING @ Mon, 03 Jun 2019 20:31:46: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:31:46: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 20:31:46: #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 20:31:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:31:48: #1 tag size is determined as 101 bps INFO @ Mon, 03 Jun 2019 20:31:48: #1 tag size = 101 INFO @ Mon, 03 Jun 2019 20:31:48: #1 total tags in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:31:48: #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 20:31:48: #1 tags after filtering in treatment: 3197520 INFO @ Mon, 03 Jun 2019 20:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:31:48: #1 finished! INFO @ Mon, 03 Jun 2019 20:31:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:31:49: #2 number of paired peaks: 3917 INFO @ Mon, 03 Jun 2019 20:31:49: start model_add_line... INFO @ Mon, 03 Jun 2019 20:31:49: start X-correlation... INFO @ Mon, 03 Jun 2019 20:31:49: end of X-cor INFO @ Mon, 03 Jun 2019 20:31:49: #2 finished! INFO @ Mon, 03 Jun 2019 20:31:49: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 20:31:49: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 20:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05_model.r WARNING @ Mon, 03 Jun 2019 20:31:49: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:31:49: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 20:31:49: #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 20:31:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:31:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.10_summits.bed INFO @ Mon, 03 Jun 2019 20:31:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4274 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:31:57: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 20:31:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.20_summits.bed INFO @ Mon, 03 Jun 2019 20:32:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2186 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482858/SRX482858.05_summits.bed INFO @ Mon, 03 Jun 2019 20:32:05: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7113 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。