Job ID = 4178586 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T04:50:21 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 ) 2019-12-05T04:50:21 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 ) 2019-12-05T05:43:15 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 ) 2019-12-05T05:51:32 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 ) 2019-12-05T05:57:56 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 ) 2019-12-05T06:03:45 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 : 81,760,468 reads read : 163,520,936 reads written : 163,520,936 rm: cannot remove ‘[DSE]RR*’: 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: 01:54:27 81760468 reads; of these: 81760468 (100.00%) were paired; of these: 58849884 (71.98%) aligned concordantly 0 times 20298086 (24.83%) aligned concordantly exactly 1 time 2612498 (3.20%) aligned concordantly >1 times ---- 58849884 pairs aligned concordantly 0 times; of these: 10138845 (17.23%) aligned discordantly 1 time ---- 48711039 pairs aligned 0 times concordantly or discordantly; of these: 97422078 mates make up the pairs; of these: 92714689 (95.17%) aligned 0 times 2326775 (2.39%) aligned exactly 1 time 2380614 (2.44%) aligned >1 times 43.30% overall alignment rate Time searching: 01:54:29 Overall time: 01:54:29 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 52 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 30177606 / 32096442 = 0.9402 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 17:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.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 @ Thu, 05 Dec 2019 17:21:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 17:21:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 17:21:53: 1000000 INFO @ Thu, 05 Dec 2019 17:22:03: 2000000 INFO @ Thu, 05 Dec 2019 17:22:12: 3000000 INFO @ Thu, 05 Dec 2019 17:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.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 @ Thu, 05 Dec 2019 17:22:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 17:22:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 17:22:22: 4000000 INFO @ Thu, 05 Dec 2019 17:22:24: 1000000 INFO @ Thu, 05 Dec 2019 17:22:32: 5000000 INFO @ Thu, 05 Dec 2019 17:22:35: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 17:22:42: 6000000 INFO @ Thu, 05 Dec 2019 17:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.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 @ Thu, 05 Dec 2019 17:22:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 17:22:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 17:22:46: 3000000 INFO @ Thu, 05 Dec 2019 17:22:53: 7000000 INFO @ Thu, 05 Dec 2019 17:22:55: 1000000 INFO @ Thu, 05 Dec 2019 17:22:56: 4000000 INFO @ Thu, 05 Dec 2019 17:23:04: 8000000 INFO @ Thu, 05 Dec 2019 17:23:07: 5000000 INFO @ Thu, 05 Dec 2019 17:23:07: 2000000 INFO @ Thu, 05 Dec 2019 17:23:15: 9000000 INFO @ Thu, 05 Dec 2019 17:23:17: 6000000 INFO @ Thu, 05 Dec 2019 17:23:18: 3000000 INFO @ Thu, 05 Dec 2019 17:23:27: 10000000 INFO @ Thu, 05 Dec 2019 17:23:28: 7000000 INFO @ Thu, 05 Dec 2019 17:23:29: 4000000 INFO @ Thu, 05 Dec 2019 17:23:32: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 17:23:32: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 17:23:32: #1 total tags in treatment: 1839149 INFO @ Thu, 05 Dec 2019 17:23:32: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 17:23:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 17:23:32: #1 tags after filtering in treatment: 1055720 INFO @ Thu, 05 Dec 2019 17:23:32: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 05 Dec 2019 17:23:32: #1 finished! INFO @ Thu, 05 Dec 2019 17:23:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 17:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 17:23:32: #2 number of paired peaks: 3738 INFO @ Thu, 05 Dec 2019 17:23:32: start model_add_line... INFO @ Thu, 05 Dec 2019 17:23:32: start X-correlation... INFO @ Thu, 05 Dec 2019 17:23:32: end of X-cor INFO @ Thu, 05 Dec 2019 17:23:32: #2 finished! INFO @ Thu, 05 Dec 2019 17:23:32: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 17:23:32: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 05 Dec 2019 17:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05_model.r INFO @ Thu, 05 Dec 2019 17:23:38: 8000000 INFO @ Thu, 05 Dec 2019 17:23:39: 5000000 WARNING @ Thu, 05 Dec 2019 17:23:41: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 17:23:41: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Thu, 05 Dec 2019 17:23:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 17:23:41: #3 Call peaks... INFO @ Thu, 05 Dec 2019 17:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 17:23:43: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 17:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05_peaks.xls INFO @ Thu, 05 Dec 2019 17:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 17:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.05_summits.bed INFO @ Thu, 05 Dec 2019 17:23:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2972 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 17:23:49: 9000000 INFO @ Thu, 05 Dec 2019 17:23:49: 6000000 INFO @ Thu, 05 Dec 2019 17:23:59: 10000000 INFO @ Thu, 05 Dec 2019 17:23:59: 7000000 INFO @ Thu, 05 Dec 2019 17:24:03: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 17:24:03: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 17:24:03: #1 total tags in treatment: 1839149 INFO @ Thu, 05 Dec 2019 17:24:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 17:24:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 17:24:03: #1 tags after filtering in treatment: 1055720 INFO @ Thu, 05 Dec 2019 17:24:03: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 05 Dec 2019 17:24:03: #1 finished! INFO @ Thu, 05 Dec 2019 17:24:03: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 17:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 17:24:04: #2 number of paired peaks: 3738 INFO @ Thu, 05 Dec 2019 17:24:04: start model_add_line... INFO @ Thu, 05 Dec 2019 17:24:04: start X-correlation... INFO @ Thu, 05 Dec 2019 17:24:04: end of X-cor INFO @ Thu, 05 Dec 2019 17:24:04: #2 finished! INFO @ Thu, 05 Dec 2019 17:24:04: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 17:24:04: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 05 Dec 2019 17:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10_model.r WARNING @ Thu, 05 Dec 2019 17:24:04: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 17:24:04: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Thu, 05 Dec 2019 17:24:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 17:24:04: #3 Call peaks... INFO @ Thu, 05 Dec 2019 17:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 17:24:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 17:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10_peaks.xls INFO @ Thu, 05 Dec 2019 17:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 17:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.10_summits.bed INFO @ Thu, 05 Dec 2019 17:24:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1471 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 17:24:10: 8000000 INFO @ Thu, 05 Dec 2019 17:24:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Dec 2019 17:24:29: 10000000 INFO @ Thu, 05 Dec 2019 17:24:34: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 17:24:34: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 17:24:34: #1 total tags in treatment: 1839149 INFO @ Thu, 05 Dec 2019 17:24:34: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 17:24:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 17:24:34: #1 tags after filtering in treatment: 1055720 INFO @ Thu, 05 Dec 2019 17:24:34: #1 Redundant rate of treatment: 0.43 INFO @ Thu, 05 Dec 2019 17:24:34: #1 finished! INFO @ Thu, 05 Dec 2019 17:24:34: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 17:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 17:24:34: #2 number of paired peaks: 3738 INFO @ Thu, 05 Dec 2019 17:24:34: start model_add_line... INFO @ Thu, 05 Dec 2019 17:24:34: start X-correlation... INFO @ Thu, 05 Dec 2019 17:24:34: end of X-cor INFO @ Thu, 05 Dec 2019 17:24:34: #2 finished! INFO @ Thu, 05 Dec 2019 17:24:34: #2 predicted fragment length is 151 bps INFO @ Thu, 05 Dec 2019 17:24:34: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 05 Dec 2019 17:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20_model.r WARNING @ Thu, 05 Dec 2019 17:24:34: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 17:24:34: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Thu, 05 Dec 2019 17:24:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 17:24:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 17:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 17:24:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 17:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20_peaks.xls INFO @ Thu, 05 Dec 2019 17:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 17:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827849/SRX5827849.20_summits.bed INFO @ Thu, 05 Dec 2019 17:24:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。