Job ID = 2011752 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:23:07 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 ) 2019-07-05T17:27:22 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 ) 2019-07-05T17:27:22 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 ) 2019-07-05T17:28:18 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 ) 2019-07-05T17:33:07 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 ) 2019-07-05T17:33:59 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 ) 2019-07-05T17:34:45 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 : 17,384,608 reads read : 34,769,216 reads written : 34,769,216 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: 00:13:17 17384608 reads; of these: 17384608 (100.00%) were paired; of these: 1343820 (7.73%) aligned concordantly 0 times 13959036 (80.30%) aligned concordantly exactly 1 time 2081752 (11.97%) aligned concordantly >1 times ---- 1343820 pairs aligned concordantly 0 times; of these: 71329 (5.31%) aligned discordantly 1 time ---- 1272491 pairs aligned 0 times concordantly or discordantly; of these: 2544982 mates make up the pairs; of these: 1677141 (65.90%) aligned 0 times 774716 (30.44%) aligned exactly 1 time 93125 (3.66%) aligned >1 times 95.18% overall alignment rate Time searching: 00:13:17 Overall time: 00:13:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 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] 11770043 / 16107033 = 0.7307 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 @ Sat, 06 Jul 2019 02:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.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, 06 Jul 2019 02:59:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:59:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.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, 06 Jul 2019 02:59:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:59:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.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, 06 Jul 2019 02:59:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:59:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:59:51: 1000000 INFO @ Sat, 06 Jul 2019 02:59:52: 1000000 INFO @ Sat, 06 Jul 2019 02:59:52: 1000000 INFO @ Sat, 06 Jul 2019 02:59:59: 2000000 INFO @ Sat, 06 Jul 2019 03:00:00: 2000000 INFO @ Sat, 06 Jul 2019 03:00:01: 2000000 INFO @ Sat, 06 Jul 2019 03:00:07: 3000000 INFO @ Sat, 06 Jul 2019 03:00:08: 3000000 INFO @ Sat, 06 Jul 2019 03:00:10: 3000000 INFO @ Sat, 06 Jul 2019 03:00:14: 4000000 INFO @ Sat, 06 Jul 2019 03:00:16: 4000000 INFO @ Sat, 06 Jul 2019 03:00:19: 4000000 INFO @ Sat, 06 Jul 2019 03:00:21: 5000000 INFO @ Sat, 06 Jul 2019 03:00:24: 5000000 INFO @ Sat, 06 Jul 2019 03:00:27: 5000000 INFO @ Sat, 06 Jul 2019 03:00:28: 6000000 INFO @ Sat, 06 Jul 2019 03:00:32: 6000000 INFO @ Sat, 06 Jul 2019 03:00:35: 7000000 INFO @ Sat, 06 Jul 2019 03:00:35: 6000000 INFO @ Sat, 06 Jul 2019 03:00:40: 7000000 INFO @ Sat, 06 Jul 2019 03:00:42: 8000000 INFO @ Sat, 06 Jul 2019 03:00:44: 7000000 INFO @ Sat, 06 Jul 2019 03:00:48: 8000000 INFO @ Sat, 06 Jul 2019 03:00:49: 9000000 INFO @ Sat, 06 Jul 2019 03:00:52: 8000000 INFO @ Sat, 06 Jul 2019 03:00:53: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 03:00:53: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 03:00:53: #1 total tags in treatment: 4284804 INFO @ Sat, 06 Jul 2019 03:00:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:00:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:00:53: #1 tags after filtering in treatment: 3200552 INFO @ Sat, 06 Jul 2019 03:00:53: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:00:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:00:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:00:53: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:00:53: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:00:53: start model_add_line... INFO @ Sat, 06 Jul 2019 03:00:53: start X-correlation... INFO @ Sat, 06 Jul 2019 03:00:53: end of X-cor INFO @ Sat, 06 Jul 2019 03:00:53: #2 finished! INFO @ Sat, 06 Jul 2019 03:00:53: #2 predicted fragment length is 113 bps INFO @ Sat, 06 Jul 2019 03:00:53: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Sat, 06 Jul 2019 03:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20_model.r INFO @ Sat, 06 Jul 2019 03:00:53: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:00:56: 9000000 INFO @ Sat, 06 Jul 2019 03:01:00: 9000000 INFO @ Sat, 06 Jul 2019 03:01:01: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 03:01:01: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 03:01:01: #1 total tags in treatment: 4284804 INFO @ Sat, 06 Jul 2019 03:01:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:01:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:01:01: #1 tags after filtering in treatment: 3200552 INFO @ Sat, 06 Jul 2019 03:01:01: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:01:01: #1 finished! INFO @ Sat, 06 Jul 2019 03:01:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:01:01: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:01:01: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:01:01: start model_add_line... INFO @ Sat, 06 Jul 2019 03:01:01: start X-correlation... INFO @ Sat, 06 Jul 2019 03:01:01: end of X-cor INFO @ Sat, 06 Jul 2019 03:01:01: #2 finished! INFO @ Sat, 06 Jul 2019 03:01:01: #2 predicted fragment length is 113 bps INFO @ Sat, 06 Jul 2019 03:01:01: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Sat, 06 Jul 2019 03:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05_model.r INFO @ Sat, 06 Jul 2019 03:01:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:01:03: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:01:05: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 03:01:05: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 03:01:05: #1 total tags in treatment: 4284804 INFO @ Sat, 06 Jul 2019 03:01:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:01:05: #1 tags after filtering in treatment: 3200552 INFO @ Sat, 06 Jul 2019 03:01:05: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 03:01:05: #1 finished! INFO @ Sat, 06 Jul 2019 03:01:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:01:05: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:01:05: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:01:05: start model_add_line... INFO @ Sat, 06 Jul 2019 03:01:05: start X-correlation... INFO @ Sat, 06 Jul 2019 03:01:05: end of X-cor INFO @ Sat, 06 Jul 2019 03:01:05: #2 finished! INFO @ Sat, 06 Jul 2019 03:01:05: #2 predicted fragment length is 113 bps INFO @ Sat, 06 Jul 2019 03:01:05: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Sat, 06 Jul 2019 03:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10_model.r INFO @ Sat, 06 Jul 2019 03:01:05: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:01:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:01:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:01:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.20_summits.bed INFO @ Sat, 06 Jul 2019 03:01:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:01:10: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.05_summits.bed INFO @ Sat, 06 Jul 2019 03:01:14: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1704 records, 4 fields): 6 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:01:15: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX497380/SRX497380.10_summits.bed INFO @ Sat, 06 Jul 2019 03:01:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。