Job ID = 1294677 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:31:44 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 ) 2019-06-03T00:32:52 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 ) 2019-06-03T00:32:52 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 ) 2019-06-03T00:32:52 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 ) 2019-06-03T00:32:52 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 ) 2019-06-03T00:34:57 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 ) 2019-06-03T00:34:57 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 ) 2019-06-03T00:39:16 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 : 22,109,731 reads read : 22,109,731 reads written : 22,109,731 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: 00:09:41 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1293868 (5.85%) aligned 0 times 13813136 (62.48%) aligned exactly 1 time 7002727 (31.67%) aligned >1 times 94.15% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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 12 files... [bam_rmdupse_core] 3521109 / 20815863 = 0.1692 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 10:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.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 10:02:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.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 10:02:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.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 10:02:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:35: 1000000 INFO @ Mon, 03 Jun 2019 10:02:37: 1000000 INFO @ Mon, 03 Jun 2019 10:02:37: 1000000 INFO @ Mon, 03 Jun 2019 10:02:44: 2000000 INFO @ Mon, 03 Jun 2019 10:02:48: 2000000 INFO @ Mon, 03 Jun 2019 10:02:48: 2000000 INFO @ Mon, 03 Jun 2019 10:02:52: 3000000 INFO @ Mon, 03 Jun 2019 10:02:58: 3000000 INFO @ Mon, 03 Jun 2019 10:02:59: 3000000 INFO @ Mon, 03 Jun 2019 10:03:00: 4000000 INFO @ Mon, 03 Jun 2019 10:03:08: 5000000 INFO @ Mon, 03 Jun 2019 10:03:08: 4000000 INFO @ Mon, 03 Jun 2019 10:03:09: 4000000 INFO @ Mon, 03 Jun 2019 10:03:16: 6000000 INFO @ Mon, 03 Jun 2019 10:03:19: 5000000 INFO @ Mon, 03 Jun 2019 10:03:19: 5000000 INFO @ Mon, 03 Jun 2019 10:03:26: 7000000 INFO @ Mon, 03 Jun 2019 10:03:30: 6000000 INFO @ Mon, 03 Jun 2019 10:03:30: 6000000 INFO @ Mon, 03 Jun 2019 10:03:35: 8000000 INFO @ Mon, 03 Jun 2019 10:03:40: 7000000 INFO @ Mon, 03 Jun 2019 10:03:41: 7000000 INFO @ Mon, 03 Jun 2019 10:03:43: 9000000 INFO @ Mon, 03 Jun 2019 10:03:51: 8000000 INFO @ Mon, 03 Jun 2019 10:03:52: 10000000 INFO @ Mon, 03 Jun 2019 10:03:52: 8000000 INFO @ Mon, 03 Jun 2019 10:04:00: 11000000 INFO @ Mon, 03 Jun 2019 10:04:01: 9000000 INFO @ Mon, 03 Jun 2019 10:04:02: 9000000 INFO @ Mon, 03 Jun 2019 10:04:09: 12000000 INFO @ Mon, 03 Jun 2019 10:04:11: 10000000 INFO @ Mon, 03 Jun 2019 10:04:12: 10000000 INFO @ Mon, 03 Jun 2019 10:04:17: 13000000 INFO @ Mon, 03 Jun 2019 10:04:21: 11000000 INFO @ Mon, 03 Jun 2019 10:04:22: 11000000 INFO @ Mon, 03 Jun 2019 10:04:25: 14000000 INFO @ Mon, 03 Jun 2019 10:04:31: 12000000 INFO @ Mon, 03 Jun 2019 10:04:32: 12000000 INFO @ Mon, 03 Jun 2019 10:04:33: 15000000 INFO @ Mon, 03 Jun 2019 10:04:41: 16000000 INFO @ Mon, 03 Jun 2019 10:04:42: 13000000 INFO @ Mon, 03 Jun 2019 10:04:43: 13000000 INFO @ Mon, 03 Jun 2019 10:04:51: 17000000 INFO @ Mon, 03 Jun 2019 10:04:52: 14000000 INFO @ Mon, 03 Jun 2019 10:04:53: 14000000 INFO @ Mon, 03 Jun 2019 10:04:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:04:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:04:54: #1 total tags in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:04:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:04:54: #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 10:04:54: #1 tags after filtering in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:04:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:04:54: #1 finished! INFO @ Mon, 03 Jun 2019 10:04:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:04:56: #2 number of paired peaks: 216 WARNING @ Mon, 03 Jun 2019 10:04:56: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 03 Jun 2019 10:04:56: start model_add_line... INFO @ Mon, 03 Jun 2019 10:04:56: start X-correlation... INFO @ Mon, 03 Jun 2019 10:04:56: end of X-cor INFO @ Mon, 03 Jun 2019 10:04:56: #2 finished! INFO @ Mon, 03 Jun 2019 10:04:56: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:04:56: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20_model.r WARNING @ Mon, 03 Jun 2019 10:04:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:04:56: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:04:56: #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 10:04:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:05:02: 15000000 INFO @ Mon, 03 Jun 2019 10:05:03: 15000000 INFO @ Mon, 03 Jun 2019 10:05:13: 16000000 INFO @ Mon, 03 Jun 2019 10:05:13: 16000000 INFO @ Mon, 03 Jun 2019 10:05:23: 17000000 INFO @ Mon, 03 Jun 2019 10:05:24: 17000000 INFO @ Mon, 03 Jun 2019 10:05:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:05:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:05:25: #1 total tags in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:05:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:05:25: #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 10:05:26: #1 tags after filtering in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:05:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:05:26: #1 finished! INFO @ Mon, 03 Jun 2019 10:05:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:05:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:05:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:05:27: #1 total tags in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:05:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:05:27: #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 10:05:27: #1 tags after filtering in treatment: 17294754 INFO @ Mon, 03 Jun 2019 10:05:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:05:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:05:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:05:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:05:27: #2 number of paired peaks: 216 WARNING @ Mon, 03 Jun 2019 10:05:27: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 03 Jun 2019 10:05:27: start model_add_line... INFO @ Mon, 03 Jun 2019 10:05:27: start X-correlation... INFO @ Mon, 03 Jun 2019 10:05:27: end of X-cor INFO @ Mon, 03 Jun 2019 10:05:27: #2 finished! INFO @ Mon, 03 Jun 2019 10:05:27: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:05:27: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:05:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10_model.r WARNING @ Mon, 03 Jun 2019 10:05:27: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:05:27: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:05:27: #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 10:05:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:05:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:05:28: #2 number of paired peaks: 216 WARNING @ Mon, 03 Jun 2019 10:05:28: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Mon, 03 Jun 2019 10:05:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:05:29: start X-correlation... INFO @ Mon, 03 Jun 2019 10:05:29: end of X-cor INFO @ Mon, 03 Jun 2019 10:05:29: #2 finished! INFO @ Mon, 03 Jun 2019 10:05:29: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:05:29: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05_model.r WARNING @ Mon, 03 Jun 2019 10:05:29: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:05:29: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:05:29: #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 10:05:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:05:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:06:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:06:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:06:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.20_summits.bed INFO @ Mon, 03 Jun 2019 10:06:03: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1356 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:06:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:06:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.10_summits.bed INFO @ Mon, 03 Jun 2019 10:06:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1837 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287818/SRX287818.05_summits.bed INFO @ Mon, 03 Jun 2019 10:06:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2185 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。