Job ID = 1294241 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:46:34 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 ) 2019-06-02T20:50:35 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 ) 2019-06-02T20:50:35 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 ) spots read : 162,513,860 reads read : 162,513,860 reads written : 162,513,860 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: 00:41:28 162513860 reads; of these: 162513860 (100.00%) were unpaired; of these: 63315678 (38.96%) aligned 0 times 74550533 (45.87%) aligned exactly 1 time 24647649 (15.17%) aligned >1 times 61.04% overall alignment rate Time searching: 00:41:28 Overall time: 00:41:28 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 44 files... [bam_rmdupse_core] 84909515 / 99198182 = 0.8560 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 06:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.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 06:56:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:56:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.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 06:56:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:56:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.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 06:56:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:56:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:56:32: 1000000 INFO @ Mon, 03 Jun 2019 06:56:32: 1000000 INFO @ Mon, 03 Jun 2019 06:56:32: 1000000 INFO @ Mon, 03 Jun 2019 06:56:43: 2000000 INFO @ Mon, 03 Jun 2019 06:56:43: 2000000 INFO @ Mon, 03 Jun 2019 06:56:43: 2000000 INFO @ Mon, 03 Jun 2019 06:56:52: 3000000 INFO @ Mon, 03 Jun 2019 06:56:54: 3000000 INFO @ Mon, 03 Jun 2019 06:56:54: 3000000 INFO @ Mon, 03 Jun 2019 06:57:03: 4000000 INFO @ Mon, 03 Jun 2019 06:57:04: 4000000 INFO @ Mon, 03 Jun 2019 06:57:05: 4000000 INFO @ Mon, 03 Jun 2019 06:57:15: 5000000 INFO @ Mon, 03 Jun 2019 06:57:15: 5000000 INFO @ Mon, 03 Jun 2019 06:57:17: 5000000 INFO @ Mon, 03 Jun 2019 06:57:25: 6000000 INFO @ Mon, 03 Jun 2019 06:57:27: 6000000 INFO @ Mon, 03 Jun 2019 06:57:28: 6000000 INFO @ Mon, 03 Jun 2019 06:57:35: 7000000 INFO @ Mon, 03 Jun 2019 06:57:38: 7000000 INFO @ Mon, 03 Jun 2019 06:57:40: 7000000 INFO @ Mon, 03 Jun 2019 06:57:45: 8000000 INFO @ Mon, 03 Jun 2019 06:57:50: 8000000 INFO @ Mon, 03 Jun 2019 06:57:51: 8000000 INFO @ Mon, 03 Jun 2019 06:57:55: 9000000 INFO @ Mon, 03 Jun 2019 06:58:01: 9000000 INFO @ Mon, 03 Jun 2019 06:58:03: 9000000 INFO @ Mon, 03 Jun 2019 06:58:05: 10000000 INFO @ Mon, 03 Jun 2019 06:58:13: 10000000 INFO @ Mon, 03 Jun 2019 06:58:14: 10000000 INFO @ Mon, 03 Jun 2019 06:58:15: 11000000 INFO @ Mon, 03 Jun 2019 06:58:25: 11000000 INFO @ Mon, 03 Jun 2019 06:58:25: 12000000 INFO @ Mon, 03 Jun 2019 06:58:26: 11000000 INFO @ Mon, 03 Jun 2019 06:58:35: 13000000 INFO @ Mon, 03 Jun 2019 06:58:36: 12000000 INFO @ Mon, 03 Jun 2019 06:58:37: 12000000 INFO @ Mon, 03 Jun 2019 06:58:45: 14000000 INFO @ Mon, 03 Jun 2019 06:58:47: 13000000 INFO @ Mon, 03 Jun 2019 06:58:48: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:58:48: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:58:48: #1 total tags in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:58:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:58:48: #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 06:58:48: #1 tags after filtering in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:58:48: #1 finished! INFO @ Mon, 03 Jun 2019 06:58:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:58:48: 13000000 INFO @ Mon, 03 Jun 2019 06:58:49: #2 number of paired peaks: 1241 INFO @ Mon, 03 Jun 2019 06:58:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:58:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:58:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:58:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:58:49: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 06:58:49: #2 alternative fragment length(s) may be 2,78,100,555 bps INFO @ Mon, 03 Jun 2019 06:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05_model.r WARNING @ Mon, 03 Jun 2019 06:58:49: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:58:49: #2 You may need to consider one of the other alternative d(s): 2,78,100,555 WARNING @ Mon, 03 Jun 2019 06:58:49: #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 06:58:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:58:57: 14000000 INFO @ Mon, 03 Jun 2019 06:58:58: 14000000 INFO @ Mon, 03 Jun 2019 06:59:00: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:59:00: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:59:00: #1 total tags in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:59:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:59:00: #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 06:59:00: #1 tags after filtering in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:59:00: #1 finished! INFO @ Mon, 03 Jun 2019 06:59:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:59:01: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:59:01: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:59:01: #1 total tags in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:59:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:59:01: #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 06:59:01: #1 tags after filtering in treatment: 14288667 INFO @ Mon, 03 Jun 2019 06:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:59:01: #1 finished! INFO @ Mon, 03 Jun 2019 06:59:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:59:02: #2 number of paired peaks: 1241 INFO @ Mon, 03 Jun 2019 06:59:02: start model_add_line... INFO @ Mon, 03 Jun 2019 06:59:02: start X-correlation... INFO @ Mon, 03 Jun 2019 06:59:02: end of X-cor INFO @ Mon, 03 Jun 2019 06:59:02: #2 finished! INFO @ Mon, 03 Jun 2019 06:59:02: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 06:59:02: #2 alternative fragment length(s) may be 2,78,100,555 bps INFO @ Mon, 03 Jun 2019 06:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10_model.r WARNING @ Mon, 03 Jun 2019 06:59:02: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:59:02: #2 You may need to consider one of the other alternative d(s): 2,78,100,555 WARNING @ Mon, 03 Jun 2019 06:59:02: #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 06:59:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:59:03: #2 number of paired peaks: 1241 INFO @ Mon, 03 Jun 2019 06:59:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:59:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:59:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:59:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:59:03: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 06:59:03: #2 alternative fragment length(s) may be 2,78,100,555 bps INFO @ Mon, 03 Jun 2019 06:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20_model.r WARNING @ Mon, 03 Jun 2019 06:59:03: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:59:03: #2 You may need to consider one of the other alternative d(s): 2,78,100,555 WARNING @ Mon, 03 Jun 2019 06:59:03: #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 06:59:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:59:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:59:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:59:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:59:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.05_summits.bed INFO @ Mon, 03 Jun 2019 06:59:50: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (15321 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.10_summits.bed INFO @ Mon, 03 Jun 2019 07:00:04: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5759 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202129/SRX202129.20_summits.bed INFO @ Mon, 03 Jun 2019 07:00:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1237 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。