Job ID = 4289150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,401,706 reads read : 14,803,412 reads written : 7,401,706 reads 0-length : 7,401,706 2019-12-10T04:45:31 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 : 12,158,622 reads read : 24,317,244 reads written : 12,158,622 reads 0-length : 12,158,622 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: 00:02:23 19560328 reads; of these: 19560328 (100.00%) were unpaired; of these: 9526537 (48.70%) aligned 0 times 4930666 (25.21%) aligned exactly 1 time 5103125 (26.09%) aligned >1 times 51.30% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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_rmdupse_core] 6369991 / 10033791 = 0.6349 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.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 @ Tue, 10 Dec 2019 13:53:42: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:53:42: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:53:52: 1000000 INFO @ Tue, 10 Dec 2019 13:54:01: 2000000 INFO @ Tue, 10 Dec 2019 13:54:10: 3000000 INFO @ Tue, 10 Dec 2019 13:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.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 @ Tue, 10 Dec 2019 13:54:12: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:54:12: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:54:16: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:54:16: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:54:16: #1 total tags in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:54:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:54:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:54:16: #1 tags after filtering in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:54:16: #1 finished! INFO @ Tue, 10 Dec 2019 13:54:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:54:16: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 13:54:16: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 13:54:16: start model_add_line... INFO @ Tue, 10 Dec 2019 13:54:16: start X-correlation... INFO @ Tue, 10 Dec 2019 13:54:16: end of X-cor INFO @ Tue, 10 Dec 2019 13:54:16: #2 finished! INFO @ Tue, 10 Dec 2019 13:54:16: #2 predicted fragment length is 0 bps INFO @ Tue, 10 Dec 2019 13:54:16: #2 alternative fragment length(s) may be 0,14,56,72,100,126,145,191,252,268,355,443,500,528 bps INFO @ Tue, 10 Dec 2019 13:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.05_model.r WARNING @ Tue, 10 Dec 2019 13:54:16: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:54:16: #2 You may need to consider one of the other alternative d(s): 0,14,56,72,100,126,145,191,252,268,355,443,500,528 WARNING @ Tue, 10 Dec 2019 13:54:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:54:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:54:22: 1000000 INFO @ Tue, 10 Dec 2019 13:54:30: 2000000 INFO @ Tue, 10 Dec 2019 13:54:39: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.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 @ Tue, 10 Dec 2019 13:54:42: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:54:42: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:54:45: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:54:45: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:54:45: #1 total tags in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:54:45: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:54:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:54:45: #1 tags after filtering in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:54:45: #1 finished! INFO @ Tue, 10 Dec 2019 13:54:45: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:54:45: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 13:54:45: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 13:54:45: start model_add_line... INFO @ Tue, 10 Dec 2019 13:54:45: start X-correlation... INFO @ Tue, 10 Dec 2019 13:54:45: end of X-cor INFO @ Tue, 10 Dec 2019 13:54:45: #2 finished! INFO @ Tue, 10 Dec 2019 13:54:45: #2 predicted fragment length is 0 bps INFO @ Tue, 10 Dec 2019 13:54:45: #2 alternative fragment length(s) may be 0,14,56,72,100,126,145,191,252,268,355,443,500,528 bps INFO @ Tue, 10 Dec 2019 13:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.10_model.r WARNING @ Tue, 10 Dec 2019 13:54:45: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:54:45: #2 You may need to consider one of the other alternative d(s): 0,14,56,72,100,126,145,191,252,268,355,443,500,528 WARNING @ Tue, 10 Dec 2019 13:54:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:54:45: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:54:52: 1000000 INFO @ Tue, 10 Dec 2019 13:55:02: 2000000 INFO @ Tue, 10 Dec 2019 13:55:11: 3000000 INFO @ Tue, 10 Dec 2019 13:55:18: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:55:18: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:55:18: #1 total tags in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:55:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:55:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:55:18: #1 tags after filtering in treatment: 3663800 INFO @ Tue, 10 Dec 2019 13:55:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:55:18: #1 finished! INFO @ Tue, 10 Dec 2019 13:55:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:55:18: #2 number of paired peaks: 115 WARNING @ Tue, 10 Dec 2019 13:55:18: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 10 Dec 2019 13:55:18: start model_add_line... INFO @ Tue, 10 Dec 2019 13:55:18: start X-correlation... INFO @ Tue, 10 Dec 2019 13:55:18: end of X-cor INFO @ Tue, 10 Dec 2019 13:55:18: #2 finished! INFO @ Tue, 10 Dec 2019 13:55:18: #2 predicted fragment length is 0 bps INFO @ Tue, 10 Dec 2019 13:55:18: #2 alternative fragment length(s) may be 0,14,56,72,100,126,145,191,252,268,355,443,500,528 bps INFO @ Tue, 10 Dec 2019 13:55:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6616766/SRX6616766.20_model.r WARNING @ Tue, 10 Dec 2019 13:55:18: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:55:18: #2 You may need to consider one of the other alternative d(s): 0,14,56,72,100,126,145,191,252,268,355,443,500,528 WARNING @ Tue, 10 Dec 2019 13:55:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:55:18: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:55:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at084/job_scripts/4289150: line 336: 22772 Terminated MACS $i /var/spool/uge/at084/job_scripts/4289150: line 336: 23055 Terminated MACS $i /var/spool/uge/at084/job_scripts/4289150: line 336: 23166 Terminated MACS $i ls: cannot access SRX6616766.05.bed: No such file or directory mv: cannot stat ‘SRX6616766.05.bed’: No such file or directory mv: cannot stat ‘SRX6616766.05.bb’: No such file or directory ls: cannot access SRX6616766.10.bed: No such file or directory mv: cannot stat ‘SRX6616766.10.bed’: No such file or directory mv: cannot stat ‘SRX6616766.10.bb’: No such file or directory ls: cannot access SRX6616766.20.bed: No such file or directory mv: cannot stat ‘SRX6616766.20.bed’: No such file or directory mv: cannot stat ‘SRX6616766.20.bb’: No such file or directory