Job ID = 2590651 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T13:56:16 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 ) 2019-08-12T13:56:16 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 ) 2019-08-12T13:56:16 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 : 25,162,813 reads read : 25,162,813 reads written : 25,162,813 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:09 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1369004 (5.44%) aligned 0 times 16619066 (66.05%) aligned exactly 1 time 7174743 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:10:09 Overall time: 00:10:09 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] 5652188 / 23793809 = 0.2375 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, 12 Aug 2019 23:23:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.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, 12 Aug 2019 23:23:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:23:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.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, 12 Aug 2019 23:23:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:23:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.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, 12 Aug 2019 23:23:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:23:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:23:19: 1000000 INFO @ Mon, 12 Aug 2019 23:23:20: 1000000 INFO @ Mon, 12 Aug 2019 23:23:20: 1000000 INFO @ Mon, 12 Aug 2019 23:23:27: 2000000 INFO @ Mon, 12 Aug 2019 23:23:27: 2000000 INFO @ Mon, 12 Aug 2019 23:23:27: 2000000 INFO @ Mon, 12 Aug 2019 23:23:34: 3000000 INFO @ Mon, 12 Aug 2019 23:23:34: 3000000 INFO @ Mon, 12 Aug 2019 23:23:34: 3000000 INFO @ Mon, 12 Aug 2019 23:23:40: 4000000 INFO @ Mon, 12 Aug 2019 23:23:41: 4000000 INFO @ Mon, 12 Aug 2019 23:23:42: 4000000 INFO @ Mon, 12 Aug 2019 23:23:46: 5000000 INFO @ Mon, 12 Aug 2019 23:23:50: 5000000 INFO @ Mon, 12 Aug 2019 23:23:51: 5000000 INFO @ Mon, 12 Aug 2019 23:23:53: 6000000 INFO @ Mon, 12 Aug 2019 23:23:59: 7000000 INFO @ Mon, 12 Aug 2019 23:23:59: 6000000 INFO @ Mon, 12 Aug 2019 23:23:59: 6000000 INFO @ Mon, 12 Aug 2019 23:24:06: 8000000 INFO @ Mon, 12 Aug 2019 23:24:06: 7000000 INFO @ Mon, 12 Aug 2019 23:24:07: 7000000 INFO @ Mon, 12 Aug 2019 23:24:12: 9000000 INFO @ Mon, 12 Aug 2019 23:24:13: 8000000 INFO @ Mon, 12 Aug 2019 23:24:15: 8000000 INFO @ Mon, 12 Aug 2019 23:24:18: 10000000 INFO @ Mon, 12 Aug 2019 23:24:20: 9000000 INFO @ Mon, 12 Aug 2019 23:24:22: 9000000 INFO @ Mon, 12 Aug 2019 23:24:25: 11000000 INFO @ Mon, 12 Aug 2019 23:24:27: 10000000 INFO @ Mon, 12 Aug 2019 23:24:30: 10000000 INFO @ Mon, 12 Aug 2019 23:24:31: 12000000 INFO @ Mon, 12 Aug 2019 23:24:34: 11000000 INFO @ Mon, 12 Aug 2019 23:24:37: 11000000 INFO @ Mon, 12 Aug 2019 23:24:37: 13000000 INFO @ Mon, 12 Aug 2019 23:24:40: 12000000 INFO @ Mon, 12 Aug 2019 23:24:44: 14000000 INFO @ Mon, 12 Aug 2019 23:24:45: 12000000 INFO @ Mon, 12 Aug 2019 23:24:49: 13000000 INFO @ Mon, 12 Aug 2019 23:24:50: 15000000 INFO @ Mon, 12 Aug 2019 23:24:53: 13000000 INFO @ Mon, 12 Aug 2019 23:24:56: 16000000 INFO @ Mon, 12 Aug 2019 23:24:59: 14000000 INFO @ Mon, 12 Aug 2019 23:25:02: 14000000 INFO @ Mon, 12 Aug 2019 23:25:03: 17000000 INFO @ Mon, 12 Aug 2019 23:25:08: 15000000 INFO @ Mon, 12 Aug 2019 23:25:09: 18000000 INFO @ Mon, 12 Aug 2019 23:25:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:25:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:25:10: #1 total tags in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:25:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:25:11: #1 tags after filtering in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:25:11: #1 finished! INFO @ Mon, 12 Aug 2019 23:25:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:25:11: 15000000 INFO @ Mon, 12 Aug 2019 23:25:12: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:25:12: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:25:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:25:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:25:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:25:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:25:12: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 23:25:12: #2 alternative fragment length(s) may be 3,43,117,156,307,393,426,461,532,537,563,587,597 bps INFO @ Mon, 12 Aug 2019 23:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20_model.r WARNING @ Mon, 12 Aug 2019 23:25:12: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:25:12: #2 You may need to consider one of the other alternative d(s): 3,43,117,156,307,393,426,461,532,537,563,587,597 WARNING @ Mon, 12 Aug 2019 23:25:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:25:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:25:18: 16000000 INFO @ Mon, 12 Aug 2019 23:25:19: 16000000 INFO @ Mon, 12 Aug 2019 23:25:27: 17000000 INFO @ Mon, 12 Aug 2019 23:25:28: 17000000 INFO @ Mon, 12 Aug 2019 23:25:35: 18000000 INFO @ Mon, 12 Aug 2019 23:25:36: 18000000 INFO @ Mon, 12 Aug 2019 23:25:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:25:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:25:36: #1 total tags in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:25:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:25:37: #1 tags after filtering in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:25:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:25:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:25:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:25:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:25:37: #1 total tags in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:25:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:25:38: #1 tags after filtering in treatment: 18141621 INFO @ Mon, 12 Aug 2019 23:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:25:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:25:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:25:38: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:25:38: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:25:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:25:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:25:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:25:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:25:39: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 23:25:39: #2 alternative fragment length(s) may be 3,43,117,156,307,393,426,461,532,537,563,587,597 bps INFO @ Mon, 12 Aug 2019 23:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10_model.r WARNING @ Mon, 12 Aug 2019 23:25:39: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:25:39: #2 You may need to consider one of the other alternative d(s): 3,43,117,156,307,393,426,461,532,537,563,587,597 WARNING @ Mon, 12 Aug 2019 23:25:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:25:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:25:39: #2 number of paired peaks: 119 WARNING @ Mon, 12 Aug 2019 23:25:39: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 12 Aug 2019 23:25:39: start model_add_line... INFO @ Mon, 12 Aug 2019 23:25:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:25:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:25:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:25:39: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 23:25:39: #2 alternative fragment length(s) may be 3,43,117,156,307,393,426,461,532,537,563,587,597 bps INFO @ Mon, 12 Aug 2019 23:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05_model.r WARNING @ Mon, 12 Aug 2019 23:25:40: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:25:40: #2 You may need to consider one of the other alternative d(s): 3,43,117,156,307,393,426,461,532,537,563,587,597 WARNING @ Mon, 12 Aug 2019 23:25:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:25:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:26:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.20_summits.bed INFO @ Mon, 12 Aug 2019 23:26:23: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:26:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:26:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.10_summits.bed INFO @ Mon, 12 Aug 2019 23:26:50: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1006 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495788/SRX495788.05_summits.bed INFO @ Mon, 12 Aug 2019 23:26:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2234 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。