Job ID = 1307558 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:22:17 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 ) 2019-06-03T13:22:46 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 ) 2019-06-03T13:22:46 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 ) 2019-06-03T13:22:46 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 ) 2019-06-03T13:25:03 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 ) 2019-06-03T13:27:34 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 ) 2019-06-03T13:27:34 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 : 18,984,480 reads read : 37,968,960 reads written : 18,984,480 reads 0-length : 18,984,480 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:05 18984480 reads; of these: 18984480 (100.00%) were unpaired; of these: 2245949 (11.83%) aligned 0 times 7809245 (41.13%) aligned exactly 1 time 8929286 (47.03%) aligned >1 times 88.17% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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] 4870790 / 16738531 = 0.2910 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 22:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.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 22:49:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.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 22:49:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.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 22:49:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:49:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:49:22: 1000000 INFO @ Mon, 03 Jun 2019 22:49:23: 1000000 INFO @ Mon, 03 Jun 2019 22:49:23: 1000000 INFO @ Mon, 03 Jun 2019 22:49:29: 2000000 INFO @ Mon, 03 Jun 2019 22:49:31: 2000000 INFO @ Mon, 03 Jun 2019 22:49:31: 2000000 INFO @ Mon, 03 Jun 2019 22:49:36: 3000000 INFO @ Mon, 03 Jun 2019 22:49:39: 3000000 INFO @ Mon, 03 Jun 2019 22:49:39: 3000000 INFO @ Mon, 03 Jun 2019 22:49:43: 4000000 INFO @ Mon, 03 Jun 2019 22:49:46: 4000000 INFO @ Mon, 03 Jun 2019 22:49:46: 4000000 INFO @ Mon, 03 Jun 2019 22:49:50: 5000000 INFO @ Mon, 03 Jun 2019 22:49:54: 5000000 INFO @ Mon, 03 Jun 2019 22:49:54: 5000000 INFO @ Mon, 03 Jun 2019 22:49:56: 6000000 INFO @ Mon, 03 Jun 2019 22:50:01: 6000000 INFO @ Mon, 03 Jun 2019 22:50:02: 6000000 INFO @ Mon, 03 Jun 2019 22:50:03: 7000000 INFO @ Mon, 03 Jun 2019 22:50:09: 7000000 INFO @ Mon, 03 Jun 2019 22:50:09: 7000000 INFO @ Mon, 03 Jun 2019 22:50:10: 8000000 INFO @ Mon, 03 Jun 2019 22:50:16: 8000000 INFO @ Mon, 03 Jun 2019 22:50:16: 8000000 INFO @ Mon, 03 Jun 2019 22:50:17: 9000000 INFO @ Mon, 03 Jun 2019 22:50:23: 10000000 INFO @ Mon, 03 Jun 2019 22:50:23: 9000000 INFO @ Mon, 03 Jun 2019 22:50:24: 9000000 INFO @ Mon, 03 Jun 2019 22:50:30: 11000000 INFO @ Mon, 03 Jun 2019 22:50:31: 10000000 INFO @ Mon, 03 Jun 2019 22:50:31: 10000000 INFO @ Mon, 03 Jun 2019 22:50:36: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:36: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:36: #1 total tags in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:36: #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 22:50:36: #1 tags after filtering in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:36: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:37: #2 number of paired peaks: 1048 INFO @ Mon, 03 Jun 2019 22:50:37: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:37: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:37: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:37: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:37: #2 predicted fragment length is 62 bps INFO @ Mon, 03 Jun 2019 22:50:37: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 03 Jun 2019 22:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10_model.r WARNING @ Mon, 03 Jun 2019 22:50:37: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:37: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 03 Jun 2019 22:50:37: #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 22:50:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:38: 11000000 INFO @ Mon, 03 Jun 2019 22:50:38: 11000000 INFO @ Mon, 03 Jun 2019 22:50:45: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:45: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:45: #1 total tags in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:45: #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 22:50:45: #1 tags after filtering in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:45: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:45: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:45: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:45: #1 total tags in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:45: #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 22:50:45: #1 tags after filtering in treatment: 11867741 INFO @ Mon, 03 Jun 2019 22:50:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:45: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:46: #2 number of paired peaks: 1048 INFO @ Mon, 03 Jun 2019 22:50:46: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:46: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:46: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:46: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:46: #2 predicted fragment length is 62 bps INFO @ Mon, 03 Jun 2019 22:50:46: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 03 Jun 2019 22:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20_model.r WARNING @ Mon, 03 Jun 2019 22:50:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:46: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 03 Jun 2019 22:50:46: #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 22:50:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:46: #2 number of paired peaks: 1048 INFO @ Mon, 03 Jun 2019 22:50:46: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:46: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:46: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:46: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:46: #2 predicted fragment length is 62 bps INFO @ Mon, 03 Jun 2019 22:50:46: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 03 Jun 2019 22:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05_model.r WARNING @ Mon, 03 Jun 2019 22:50:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:46: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 03 Jun 2019 22:50:46: #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 22:50:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:51:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.10_summits.bed INFO @ Mon, 03 Jun 2019 22:51:26: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2365 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.20_summits.bed INFO @ Mon, 03 Jun 2019 22:51:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1203 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343094/SRX5343094.05_summits.bed INFO @ Mon, 03 Jun 2019 22:51:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6003 records, 4 fields): 102 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。