Job ID = 2641227 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T13:07:07 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 ) 2019-08-24T13:07:07 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 ) 2019-08-24T13:07:07 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 : 20,172,258 reads read : 40,344,516 reads written : 40,344,516 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: 00:17:28 20172258 reads; of these: 20172258 (100.00%) were paired; of these: 17159445 (85.06%) aligned concordantly 0 times 1453183 (7.20%) aligned concordantly exactly 1 time 1559630 (7.73%) aligned concordantly >1 times ---- 17159445 pairs aligned concordantly 0 times; of these: 704675 (4.11%) aligned discordantly 1 time ---- 16454770 pairs aligned 0 times concordantly or discordantly; of these: 32909540 mates make up the pairs; of these: 23566525 (71.61%) aligned 0 times 5351409 (16.26%) aligned exactly 1 time 3991606 (12.13%) aligned >1 times 41.59% overall alignment rate Time searching: 00:17:28 Overall time: 00:17:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1795064 / 3416355 = 0.5254 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 22:34:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:34:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:34:20: 1000000 INFO @ Sat, 24 Aug 2019 22:34:27: 2000000 INFO @ Sat, 24 Aug 2019 22:34:34: 3000000 INFO @ Sat, 24 Aug 2019 22:34:42: 4000000 INFO @ Sat, 24 Aug 2019 22:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 22:34:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:34:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:34:48: 1000000 INFO @ Sat, 24 Aug 2019 22:34:49: 5000000 INFO @ Sat, 24 Aug 2019 22:34:55: 2000000 INFO @ Sat, 24 Aug 2019 22:34:57: 6000000 INFO @ Sat, 24 Aug 2019 22:35:01: 3000000 INFO @ Sat, 24 Aug 2019 22:35:05: 7000000 INFO @ Sat, 24 Aug 2019 22:35:07: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 22:35:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:35:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:35:12: 8000000 INFO @ Sat, 24 Aug 2019 22:35:13: 5000000 INFO @ Sat, 24 Aug 2019 22:35:19: 6000000 INFO @ Sat, 24 Aug 2019 22:35:19: 1000000 INFO @ Sat, 24 Aug 2019 22:35:20: 9000000 INFO @ Sat, 24 Aug 2019 22:35:25: 7000000 INFO @ Sat, 24 Aug 2019 22:35:27: 2000000 INFO @ Sat, 24 Aug 2019 22:35:27: 10000000 INFO @ Sat, 24 Aug 2019 22:35:31: 8000000 INFO @ Sat, 24 Aug 2019 22:35:34: 3000000 INFO @ Sat, 24 Aug 2019 22:35:34: 11000000 INFO @ Sat, 24 Aug 2019 22:35:37: 9000000 INFO @ Sat, 24 Aug 2019 22:35:41: 4000000 INFO @ Sat, 24 Aug 2019 22:35:41: 12000000 INFO @ Sat, 24 Aug 2019 22:35:43: 10000000 INFO @ Sat, 24 Aug 2019 22:35:48: 5000000 INFO @ Sat, 24 Aug 2019 22:35:48: 13000000 INFO @ Sat, 24 Aug 2019 22:35:49: 11000000 INFO @ Sat, 24 Aug 2019 22:35:50: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 22:35:50: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 22:35:50: #1 total tags in treatment: 1393295 INFO @ Sat, 24 Aug 2019 22:35:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:35:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:35:50: #1 tags after filtering in treatment: 543791 INFO @ Sat, 24 Aug 2019 22:35:50: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:35:50: #1 finished! INFO @ Sat, 24 Aug 2019 22:35:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:35:50: #2 number of paired peaks: 439 WARNING @ Sat, 24 Aug 2019 22:35:50: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sat, 24 Aug 2019 22:35:50: start model_add_line... INFO @ Sat, 24 Aug 2019 22:35:50: start X-correlation... INFO @ Sat, 24 Aug 2019 22:35:50: end of X-cor INFO @ Sat, 24 Aug 2019 22:35:50: #2 finished! INFO @ Sat, 24 Aug 2019 22:35:50: #2 predicted fragment length is 222 bps INFO @ Sat, 24 Aug 2019 22:35:50: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 24 Aug 2019 22:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05_model.r INFO @ Sat, 24 Aug 2019 22:35:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:35:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05_peaks.xls INFO @ Sat, 24 Aug 2019 22:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.05_summits.bed INFO @ Sat, 24 Aug 2019 22:35:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:35:54: 6000000 INFO @ Sat, 24 Aug 2019 22:35:55: 12000000 INFO @ Sat, 24 Aug 2019 22:36:00: 7000000 INFO @ Sat, 24 Aug 2019 22:36:01: 13000000 INFO @ Sat, 24 Aug 2019 22:36:02: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 22:36:02: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 22:36:02: #1 total tags in treatment: 1393295 INFO @ Sat, 24 Aug 2019 22:36:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:36:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:36:02: #1 tags after filtering in treatment: 543791 INFO @ Sat, 24 Aug 2019 22:36:02: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:36:02: #1 finished! INFO @ Sat, 24 Aug 2019 22:36:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:36:02: #2 number of paired peaks: 439 WARNING @ Sat, 24 Aug 2019 22:36:02: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sat, 24 Aug 2019 22:36:02: start model_add_line... INFO @ Sat, 24 Aug 2019 22:36:02: start X-correlation... INFO @ Sat, 24 Aug 2019 22:36:02: end of X-cor INFO @ Sat, 24 Aug 2019 22:36:02: #2 finished! INFO @ Sat, 24 Aug 2019 22:36:02: #2 predicted fragment length is 222 bps INFO @ Sat, 24 Aug 2019 22:36:02: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 24 Aug 2019 22:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10_model.r INFO @ Sat, 24 Aug 2019 22:36:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:36:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10_peaks.xls INFO @ Sat, 24 Aug 2019 22:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.10_summits.bed INFO @ Sat, 24 Aug 2019 22:36:06: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:36:07: 8000000 INFO @ Sat, 24 Aug 2019 22:36:13: 9000000 INFO @ Sat, 24 Aug 2019 22:36:19: 10000000 INFO @ Sat, 24 Aug 2019 22:36:25: 11000000 INFO @ Sat, 24 Aug 2019 22:36:31: 12000000 INFO @ Sat, 24 Aug 2019 22:36:37: 13000000 INFO @ Sat, 24 Aug 2019 22:36:38: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 22:36:38: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 22:36:38: #1 total tags in treatment: 1393295 INFO @ Sat, 24 Aug 2019 22:36:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:36:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:36:38: #1 tags after filtering in treatment: 543791 INFO @ Sat, 24 Aug 2019 22:36:38: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 24 Aug 2019 22:36:38: #1 finished! INFO @ Sat, 24 Aug 2019 22:36:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:36:38: #2 number of paired peaks: 439 WARNING @ Sat, 24 Aug 2019 22:36:38: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sat, 24 Aug 2019 22:36:38: start model_add_line... INFO @ Sat, 24 Aug 2019 22:36:38: start X-correlation... INFO @ Sat, 24 Aug 2019 22:36:38: end of X-cor INFO @ Sat, 24 Aug 2019 22:36:38: #2 finished! INFO @ Sat, 24 Aug 2019 22:36:38: #2 predicted fragment length is 222 bps INFO @ Sat, 24 Aug 2019 22:36:38: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 24 Aug 2019 22:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20_model.r INFO @ Sat, 24 Aug 2019 22:36:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:36:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20_peaks.xls INFO @ Sat, 24 Aug 2019 22:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820061/SRX5820061.20_summits.bed INFO @ Sat, 24 Aug 2019 22:36:42: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。