Job ID = 1300562 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:18:03 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 ) 2019-06-03T10:18:04 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 ) 2019-06-03T10:22:08 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 ) 2019-06-03T10:22:08 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 ) 2019-06-03T10:23:31 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 ) 2019-06-03T10:27:19 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 ) 2019-06-03T10:27:19 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 : 41,239,710 reads read : 41,239,710 reads written : 41,239,710 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: 00:20:24 41239710 reads; of these: 41239710 (100.00%) were unpaired; of these: 3925791 (9.52%) aligned 0 times 26010105 (63.07%) aligned exactly 1 time 11303814 (27.41%) aligned >1 times 90.48% overall alignment rate Time searching: 00:20:24 Overall time: 00:20:24 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 16 files... [bam_rmdupse_core] 21729691 / 37313919 = 0.5823 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 20:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.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 20:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.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 20:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.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 20:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:49: 1000000 INFO @ Mon, 03 Jun 2019 20:00:50: 1000000 INFO @ Mon, 03 Jun 2019 20:00:51: 1000000 INFO @ Mon, 03 Jun 2019 20:00:58: 2000000 INFO @ Mon, 03 Jun 2019 20:00:59: 2000000 INFO @ Mon, 03 Jun 2019 20:01:03: 2000000 INFO @ Mon, 03 Jun 2019 20:01:07: 3000000 INFO @ Mon, 03 Jun 2019 20:01:09: 3000000 INFO @ Mon, 03 Jun 2019 20:01:14: 3000000 INFO @ Mon, 03 Jun 2019 20:01:16: 4000000 INFO @ Mon, 03 Jun 2019 20:01:19: 4000000 INFO @ Mon, 03 Jun 2019 20:01:25: 5000000 INFO @ Mon, 03 Jun 2019 20:01:25: 4000000 INFO @ Mon, 03 Jun 2019 20:01:28: 5000000 INFO @ Mon, 03 Jun 2019 20:01:33: 6000000 INFO @ Mon, 03 Jun 2019 20:01:36: 5000000 INFO @ Mon, 03 Jun 2019 20:01:38: 6000000 INFO @ Mon, 03 Jun 2019 20:01:42: 7000000 INFO @ Mon, 03 Jun 2019 20:01:47: 7000000 INFO @ Mon, 03 Jun 2019 20:01:48: 6000000 INFO @ Mon, 03 Jun 2019 20:01:50: 8000000 INFO @ Mon, 03 Jun 2019 20:01:57: 8000000 INFO @ Mon, 03 Jun 2019 20:01:59: 9000000 INFO @ Mon, 03 Jun 2019 20:01:59: 7000000 INFO @ Mon, 03 Jun 2019 20:02:06: 9000000 INFO @ Mon, 03 Jun 2019 20:02:07: 10000000 INFO @ Mon, 03 Jun 2019 20:02:10: 8000000 INFO @ Mon, 03 Jun 2019 20:02:16: 11000000 INFO @ Mon, 03 Jun 2019 20:02:16: 10000000 INFO @ Mon, 03 Jun 2019 20:02:21: 9000000 INFO @ Mon, 03 Jun 2019 20:02:24: 12000000 INFO @ Mon, 03 Jun 2019 20:02:25: 11000000 INFO @ Mon, 03 Jun 2019 20:02:33: 10000000 INFO @ Mon, 03 Jun 2019 20:02:33: 13000000 INFO @ Mon, 03 Jun 2019 20:02:35: 12000000 INFO @ Mon, 03 Jun 2019 20:02:42: 14000000 INFO @ Mon, 03 Jun 2019 20:02:44: 11000000 INFO @ Mon, 03 Jun 2019 20:02:44: 13000000 INFO @ Mon, 03 Jun 2019 20:02:50: 15000000 INFO @ Mon, 03 Jun 2019 20:02:53: 14000000 INFO @ Mon, 03 Jun 2019 20:02:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:02:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:02:55: #1 total tags in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:02:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:02:55: #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 20:02:55: 12000000 INFO @ Mon, 03 Jun 2019 20:02:56: #1 tags after filtering in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:02:56: #1 finished! INFO @ Mon, 03 Jun 2019 20:02:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:02:57: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 20:02:57: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 20:02:57: start model_add_line... INFO @ Mon, 03 Jun 2019 20:02:57: start X-correlation... INFO @ Mon, 03 Jun 2019 20:02:57: end of X-cor INFO @ Mon, 03 Jun 2019 20:02:57: #2 finished! INFO @ Mon, 03 Jun 2019 20:02:57: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 20:02:57: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 20:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10_model.r WARNING @ Mon, 03 Jun 2019 20:02:57: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:02:57: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 20:02:57: #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 20:02:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:03:02: 15000000 INFO @ Mon, 03 Jun 2019 20:03:06: 13000000 INFO @ Mon, 03 Jun 2019 20:03:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:03:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:03:08: #1 total tags in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:03:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:03:08: #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 20:03:08: #1 tags after filtering in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:03:08: #1 finished! INFO @ Mon, 03 Jun 2019 20:03:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:03:10: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 20:03:10: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 20:03:10: start model_add_line... INFO @ Mon, 03 Jun 2019 20:03:10: start X-correlation... INFO @ Mon, 03 Jun 2019 20:03:10: end of X-cor INFO @ Mon, 03 Jun 2019 20:03:10: #2 finished! INFO @ Mon, 03 Jun 2019 20:03:10: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 20:03:10: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 20:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05_model.r WARNING @ Mon, 03 Jun 2019 20:03:10: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:03:10: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 20:03:10: #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 20:03:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:03:17: 14000000 INFO @ Mon, 03 Jun 2019 20:03:27: 15000000 INFO @ Mon, 03 Jun 2019 20:03:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:03:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:03:33: #1 total tags in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:03:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:03:33: #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 20:03:33: #1 tags after filtering in treatment: 15584228 INFO @ Mon, 03 Jun 2019 20:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:03:33: #1 finished! INFO @ Mon, 03 Jun 2019 20:03:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:03:35: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 20:03:35: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 20:03:35: start model_add_line... INFO @ Mon, 03 Jun 2019 20:03:35: start X-correlation... INFO @ Mon, 03 Jun 2019 20:03:35: end of X-cor INFO @ Mon, 03 Jun 2019 20:03:35: #2 finished! INFO @ Mon, 03 Jun 2019 20:03:35: #2 predicted fragment length is 71 bps INFO @ Mon, 03 Jun 2019 20:03:35: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 03 Jun 2019 20:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20_model.r WARNING @ Mon, 03 Jun 2019 20:03:35: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:03:35: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 03 Jun 2019 20:03:35: #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 20:03:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:03:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:03:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.10_summits.bed INFO @ Mon, 03 Jun 2019 20:04:06: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6176 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:04:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.05_summits.bed INFO @ Mon, 03 Jun 2019 20:04:20: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12900 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823784/SRX4823784.20_summits.bed INFO @ Mon, 03 Jun 2019 20:04:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2580 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。