Job ID = 4178537 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:48:21 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 ) 2019-12-05T03:48:21 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 ) 2019-12-05T03:48:21 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 ) spots read : 11,826,614 reads read : 11,826,614 reads written : 11,826,614 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: 00:05:17 11826614 reads; of these: 11826614 (100.00%) were unpaired; of these: 211109 (1.79%) aligned 0 times 9302782 (78.66%) aligned exactly 1 time 2312723 (19.56%) aligned >1 times 98.21% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 2299878 / 11615505 = 0.1980 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.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 13:00:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:35: 1000000 INFO @ Thu, 05 Dec 2019 13:00:44: 2000000 INFO @ Thu, 05 Dec 2019 13:00:54: 3000000 INFO @ Thu, 05 Dec 2019 13:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.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 13:00:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:01:06: 4000000 INFO @ Thu, 05 Dec 2019 13:01:07: 1000000 INFO @ Thu, 05 Dec 2019 13:01:18: 5000000 INFO @ Thu, 05 Dec 2019 13:01:20: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.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 13:01:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:01:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:01:30: 6000000 INFO @ Thu, 05 Dec 2019 13:01:33: 3000000 INFO @ Thu, 05 Dec 2019 13:01:36: 1000000 INFO @ Thu, 05 Dec 2019 13:01:43: 7000000 INFO @ Thu, 05 Dec 2019 13:01:45: 4000000 INFO @ Thu, 05 Dec 2019 13:01:46: 2000000 INFO @ Thu, 05 Dec 2019 13:01:56: 8000000 INFO @ Thu, 05 Dec 2019 13:01:57: 3000000 INFO @ Thu, 05 Dec 2019 13:01:58: 5000000 INFO @ Thu, 05 Dec 2019 13:02:08: 9000000 INFO @ Thu, 05 Dec 2019 13:02:08: 4000000 INFO @ Thu, 05 Dec 2019 13:02:12: 6000000 INFO @ Thu, 05 Dec 2019 13:02:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:02:12: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:02:12: #1 total tags in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:02:12: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:02:12: #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 13:02:12: #1 tags after filtering in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:02:12: #1 finished! INFO @ Thu, 05 Dec 2019 13:02:12: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:02:13: #2 number of paired peaks: 217 WARNING @ Thu, 05 Dec 2019 13:02:13: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Thu, 05 Dec 2019 13:02:13: start model_add_line... INFO @ Thu, 05 Dec 2019 13:02:13: start X-correlation... INFO @ Thu, 05 Dec 2019 13:02:13: end of X-cor INFO @ Thu, 05 Dec 2019 13:02:13: #2 finished! INFO @ Thu, 05 Dec 2019 13:02:13: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 13:02:13: #2 alternative fragment length(s) may be 35,89,107,126,167,193,262,287,454,483,498,521 bps INFO @ Thu, 05 Dec 2019 13:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05_model.r WARNING @ Thu, 05 Dec 2019 13:02:13: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:02:13: #2 You may need to consider one of the other alternative d(s): 35,89,107,126,167,193,262,287,454,483,498,521 WARNING @ Thu, 05 Dec 2019 13:02:13: #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 13:02:13: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:19: 5000000 INFO @ Thu, 05 Dec 2019 13:02:24: 7000000 INFO @ Thu, 05 Dec 2019 13:02:29: 6000000 INFO @ Thu, 05 Dec 2019 13:02:36: 8000000 INFO @ Thu, 05 Dec 2019 13:02:40: 7000000 INFO @ Thu, 05 Dec 2019 13:02:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:02:48: 9000000 INFO @ Thu, 05 Dec 2019 13:02:50: 8000000 INFO @ Thu, 05 Dec 2019 13:02:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:02:52: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:02:52: #1 total tags in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:02:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:02:52: #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 13:02:52: #1 tags after filtering in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:02:52: #1 finished! INFO @ Thu, 05 Dec 2019 13:02:52: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:02:53: #2 number of paired peaks: 217 WARNING @ Thu, 05 Dec 2019 13:02:53: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Thu, 05 Dec 2019 13:02:53: start model_add_line... INFO @ Thu, 05 Dec 2019 13:02:53: start X-correlation... INFO @ Thu, 05 Dec 2019 13:02:53: end of X-cor INFO @ Thu, 05 Dec 2019 13:02:53: #2 finished! INFO @ Thu, 05 Dec 2019 13:02:53: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 13:02:53: #2 alternative fragment length(s) may be 35,89,107,126,167,193,262,287,454,483,498,521 bps INFO @ Thu, 05 Dec 2019 13:02:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10_model.r WARNING @ Thu, 05 Dec 2019 13:02:53: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:02:53: #2 You may need to consider one of the other alternative d(s): 35,89,107,126,167,193,262,287,454,483,498,521 WARNING @ Thu, 05 Dec 2019 13:02:53: #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 13:02:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.05_summits.bed INFO @ Thu, 05 Dec 2019 13:02:55: Done! pass1 - making usageList (13 chroms): 11 millis pass2 - checking and writing primary data (951 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:12: 9000000 INFO @ Thu, 05 Dec 2019 13:03:15: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:03:15: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:03:15: #1 total tags in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:03:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:03:15: #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 13:03:16: #1 tags after filtering in treatment: 9315627 INFO @ Thu, 05 Dec 2019 13:03:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:03:16: #1 finished! INFO @ Thu, 05 Dec 2019 13:03:16: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:03:18: #2 number of paired peaks: 217 WARNING @ Thu, 05 Dec 2019 13:03:18: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Thu, 05 Dec 2019 13:03:18: start model_add_line... INFO @ Thu, 05 Dec 2019 13:03:18: start X-correlation... INFO @ Thu, 05 Dec 2019 13:03:18: end of X-cor INFO @ Thu, 05 Dec 2019 13:03:18: #2 finished! INFO @ Thu, 05 Dec 2019 13:03:18: #2 predicted fragment length is 89 bps INFO @ Thu, 05 Dec 2019 13:03:18: #2 alternative fragment length(s) may be 35,89,107,126,167,193,262,287,454,483,498,521 bps INFO @ Thu, 05 Dec 2019 13:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20_model.r WARNING @ Thu, 05 Dec 2019 13:03:19: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:03:19: #2 You may need to consider one of the other alternative d(s): 35,89,107,126,167,193,262,287,454,483,498,521 WARNING @ Thu, 05 Dec 2019 13:03:19: #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 13:03:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:03:29: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:03:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:03:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:03:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.10_summits.bed INFO @ Thu, 05 Dec 2019 13:03:47: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (293 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:50: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736588/SRX5736588.20_summits.bed INFO @ Thu, 05 Dec 2019 13:04:11: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。