Job ID = 1306833 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:59:35 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 ) 2019-06-03T13:05:26 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 : 24,727,664 reads read : 24,727,664 reads written : 24,727,664 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: 00:09:40 24727664 reads; of these: 24727664 (100.00%) were unpaired; of these: 719997 (2.91%) aligned 0 times 15641722 (63.26%) aligned exactly 1 time 8365945 (33.83%) aligned >1 times 97.09% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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] 3272425 / 24007667 = 0.1363 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 22:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.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 22:23:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:23:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.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 22:23:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:23:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.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 22:23:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:23:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:23:49: 1000000 INFO @ Mon, 03 Jun 2019 22:23:49: 1000000 INFO @ Mon, 03 Jun 2019 22:23:51: 1000000 INFO @ Mon, 03 Jun 2019 22:23:55: 2000000 INFO @ Mon, 03 Jun 2019 22:23:57: 2000000 INFO @ Mon, 03 Jun 2019 22:24:00: 2000000 INFO @ Mon, 03 Jun 2019 22:24:02: 3000000 INFO @ Mon, 03 Jun 2019 22:24:06: 3000000 INFO @ Mon, 03 Jun 2019 22:24:09: 3000000 INFO @ Mon, 03 Jun 2019 22:24:10: 4000000 INFO @ Mon, 03 Jun 2019 22:24:15: 4000000 INFO @ Mon, 03 Jun 2019 22:24:17: 4000000 INFO @ Mon, 03 Jun 2019 22:24:18: 5000000 INFO @ Mon, 03 Jun 2019 22:24:23: 5000000 INFO @ Mon, 03 Jun 2019 22:24:25: 5000000 INFO @ Mon, 03 Jun 2019 22:24:26: 6000000 INFO @ Mon, 03 Jun 2019 22:24:32: 6000000 INFO @ Mon, 03 Jun 2019 22:24:34: 7000000 INFO @ Mon, 03 Jun 2019 22:24:34: 6000000 INFO @ Mon, 03 Jun 2019 22:24:41: 7000000 INFO @ Mon, 03 Jun 2019 22:24:41: 8000000 INFO @ Mon, 03 Jun 2019 22:24:44: 7000000 INFO @ Mon, 03 Jun 2019 22:24:50: 8000000 INFO @ Mon, 03 Jun 2019 22:24:50: 9000000 INFO @ Mon, 03 Jun 2019 22:24:53: 8000000 INFO @ Mon, 03 Jun 2019 22:24:58: 10000000 INFO @ Mon, 03 Jun 2019 22:24:58: 9000000 INFO @ Mon, 03 Jun 2019 22:25:01: 9000000 INFO @ Mon, 03 Jun 2019 22:25:05: 11000000 INFO @ Mon, 03 Jun 2019 22:25:07: 10000000 INFO @ Mon, 03 Jun 2019 22:25:09: 10000000 INFO @ Mon, 03 Jun 2019 22:25:13: 12000000 INFO @ Mon, 03 Jun 2019 22:25:15: 11000000 INFO @ Mon, 03 Jun 2019 22:25:18: 11000000 INFO @ Mon, 03 Jun 2019 22:25:21: 13000000 INFO @ Mon, 03 Jun 2019 22:25:24: 12000000 INFO @ Mon, 03 Jun 2019 22:25:27: 12000000 INFO @ Mon, 03 Jun 2019 22:25:29: 14000000 INFO @ Mon, 03 Jun 2019 22:25:33: 13000000 INFO @ Mon, 03 Jun 2019 22:25:35: 13000000 INFO @ Mon, 03 Jun 2019 22:25:36: 15000000 INFO @ Mon, 03 Jun 2019 22:25:42: 14000000 INFO @ Mon, 03 Jun 2019 22:25:43: 16000000 INFO @ Mon, 03 Jun 2019 22:25:44: 14000000 INFO @ Mon, 03 Jun 2019 22:25:50: 17000000 INFO @ Mon, 03 Jun 2019 22:25:50: 15000000 INFO @ Mon, 03 Jun 2019 22:25:52: 15000000 INFO @ Mon, 03 Jun 2019 22:25:57: 18000000 INFO @ Mon, 03 Jun 2019 22:25:59: 16000000 INFO @ Mon, 03 Jun 2019 22:26:01: 16000000 INFO @ Mon, 03 Jun 2019 22:26:04: 19000000 INFO @ Mon, 03 Jun 2019 22:26:07: 17000000 INFO @ Mon, 03 Jun 2019 22:26:09: 17000000 INFO @ Mon, 03 Jun 2019 22:26:11: 20000000 INFO @ Mon, 03 Jun 2019 22:26:16: 18000000 INFO @ Mon, 03 Jun 2019 22:26:16: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 22:26:16: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 22:26:16: #1 total tags in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:26:16: #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 22:26:17: #1 tags after filtering in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:26:17: #1 finished! INFO @ Mon, 03 Jun 2019 22:26:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:26:18: 18000000 INFO @ Mon, 03 Jun 2019 22:26:19: #2 number of paired peaks: 758 WARNING @ Mon, 03 Jun 2019 22:26:19: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Mon, 03 Jun 2019 22:26:19: start model_add_line... INFO @ Mon, 03 Jun 2019 22:26:19: start X-correlation... INFO @ Mon, 03 Jun 2019 22:26:19: end of X-cor INFO @ Mon, 03 Jun 2019 22:26:19: #2 finished! INFO @ Mon, 03 Jun 2019 22:26:19: #2 predicted fragment length is 37 bps INFO @ Mon, 03 Jun 2019 22:26:19: #2 alternative fragment length(s) may be 2,37 bps INFO @ Mon, 03 Jun 2019 22:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05_model.r WARNING @ Mon, 03 Jun 2019 22:26:19: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:26:19: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Mon, 03 Jun 2019 22:26:19: #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 22:26:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:26:24: 19000000 INFO @ Mon, 03 Jun 2019 22:26:26: 19000000 INFO @ Mon, 03 Jun 2019 22:26:32: 20000000 INFO @ Mon, 03 Jun 2019 22:26:34: 20000000 INFO @ Mon, 03 Jun 2019 22:26:38: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 22:26:38: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 22:26:38: #1 total tags in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:26:38: #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 22:26:39: #1 tags after filtering in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:26:39: #1 finished! INFO @ Mon, 03 Jun 2019 22:26:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:26:40: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 22:26:40: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 22:26:40: #1 total tags in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:26:40: #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 22:26:41: #2 number of paired peaks: 758 WARNING @ Mon, 03 Jun 2019 22:26:41: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Mon, 03 Jun 2019 22:26:41: start model_add_line... INFO @ Mon, 03 Jun 2019 22:26:41: start X-correlation... INFO @ Mon, 03 Jun 2019 22:26:41: end of X-cor INFO @ Mon, 03 Jun 2019 22:26:41: #2 finished! INFO @ Mon, 03 Jun 2019 22:26:41: #2 predicted fragment length is 37 bps INFO @ Mon, 03 Jun 2019 22:26:41: #2 alternative fragment length(s) may be 2,37 bps INFO @ Mon, 03 Jun 2019 22:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20_model.r WARNING @ Mon, 03 Jun 2019 22:26:41: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:26:41: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Mon, 03 Jun 2019 22:26:41: #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 22:26:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:26:41: #1 tags after filtering in treatment: 20735242 INFO @ Mon, 03 Jun 2019 22:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:26:41: #1 finished! INFO @ Mon, 03 Jun 2019 22:26:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:26:43: #2 number of paired peaks: 758 WARNING @ Mon, 03 Jun 2019 22:26:43: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Mon, 03 Jun 2019 22:26:43: start model_add_line... INFO @ Mon, 03 Jun 2019 22:26:43: start X-correlation... INFO @ Mon, 03 Jun 2019 22:26:43: end of X-cor INFO @ Mon, 03 Jun 2019 22:26:43: #2 finished! INFO @ Mon, 03 Jun 2019 22:26:43: #2 predicted fragment length is 37 bps INFO @ Mon, 03 Jun 2019 22:26:43: #2 alternative fragment length(s) may be 2,37 bps INFO @ Mon, 03 Jun 2019 22:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10_model.r WARNING @ Mon, 03 Jun 2019 22:26:43: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:26:43: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Mon, 03 Jun 2019 22:26:43: #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 22:26:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:27:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:27:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:27:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.05_summits.bed INFO @ Mon, 03 Jun 2019 22:27:37: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5018 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.20_summits.bed INFO @ Mon, 03 Jun 2019 22:27:58: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1200 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511124/SRX511124.10_summits.bed INFO @ Mon, 03 Jun 2019 22:28:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3126 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。