Job ID = 5790824 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,904,935 reads read : 4,904,935 reads written : 4,904,935 spots read : 4,648,300 reads read : 4,648,300 reads written : 4,648,300 2020-04-21T22:50:01 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 : 4,627,880 reads read : 4,627,880 reads written : 4,627,880 spots read : 4,443,912 reads read : 4,443,912 reads written : 4,443,912 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: 00:02:42 18625027 reads; of these: 18625027 (100.00%) were unpaired; of these: 473734 (2.54%) aligned 0 times 15533676 (83.40%) aligned exactly 1 time 2617617 (14.05%) aligned >1 times 97.46% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 17663297 / 18151293 = 0.9731 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.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 @ Wed, 22 Apr 2020 07:59:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:29: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:59:29: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:59:29: #1 total tags in treatment: 487996 INFO @ Wed, 22 Apr 2020 07:59:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:59:29: #1 tags after filtering in treatment: 487996 INFO @ Wed, 22 Apr 2020 07:59:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:29: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:29: #2 number of paired peaks: 453 WARNING @ Wed, 22 Apr 2020 07:59:29: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:29: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:29: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:29: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:29: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:29: #2 predicted fragment length is 85 bps INFO @ Wed, 22 Apr 2020 07:59:29: #2 alternative fragment length(s) may be 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 bps INFO @ Wed, 22 Apr 2020 07:59:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05_model.r WARNING @ Wed, 22 Apr 2020 07:59:29: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:29: #2 You may need to consider one of the other alternative d(s): 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 WARNING @ Wed, 22 Apr 2020 07:59:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:59:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:59:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.05_summits.bed INFO @ Wed, 22 Apr 2020 07:59:31: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 07:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.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 @ Wed, 22 Apr 2020 07:59:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:59: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:59:59: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:59:59: #1 total tags in treatment: 487996 INFO @ Wed, 22 Apr 2020 07:59:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:59:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:59:59: #1 tags after filtering in treatment: 487996 INFO @ Wed, 22 Apr 2020 07:59:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:59:59: #1 finished! INFO @ Wed, 22 Apr 2020 07:59:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:59:59: #2 number of paired peaks: 453 WARNING @ Wed, 22 Apr 2020 07:59:59: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Wed, 22 Apr 2020 07:59:59: start model_add_line... INFO @ Wed, 22 Apr 2020 07:59:59: start X-correlation... INFO @ Wed, 22 Apr 2020 07:59:59: end of X-cor INFO @ Wed, 22 Apr 2020 07:59:59: #2 finished! INFO @ Wed, 22 Apr 2020 07:59:59: #2 predicted fragment length is 85 bps INFO @ Wed, 22 Apr 2020 07:59:59: #2 alternative fragment length(s) may be 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 bps INFO @ Wed, 22 Apr 2020 07:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10_model.r WARNING @ Wed, 22 Apr 2020 07:59:59: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:59:59: #2 You may need to consider one of the other alternative d(s): 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 WARNING @ Wed, 22 Apr 2020 07:59:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:59:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:00: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.10_summits.bed INFO @ Wed, 22 Apr 2020 08:00:01: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (52 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.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 @ Wed, 22 Apr 2020 08:00:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:29: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 08:00:29: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 08:00:29: #1 total tags in treatment: 487996 INFO @ Wed, 22 Apr 2020 08:00:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:00:29: #1 tags after filtering in treatment: 487996 INFO @ Wed, 22 Apr 2020 08:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:00:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:29: #2 number of paired peaks: 453 WARNING @ Wed, 22 Apr 2020 08:00:29: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:29: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:29: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:29: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:29: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:29: #2 predicted fragment length is 85 bps INFO @ Wed, 22 Apr 2020 08:00:29: #2 alternative fragment length(s) may be 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 bps INFO @ Wed, 22 Apr 2020 08:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20_model.r WARNING @ Wed, 22 Apr 2020 08:00:29: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:00:29: #2 You may need to consider one of the other alternative d(s): 4,67,85,97,144,190,220,240,246,255,278,403,428,436,441,466,485,504,545,581 WARNING @ Wed, 22 Apr 2020 08:00:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:00:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858301/ERX2858301.20_summits.bed INFO @ Wed, 22 Apr 2020 08:00:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。