Job ID = 5720998 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:35:42 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 : 24,025,518 reads read : 24,025,518 reads written : 24,025,518 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: 00:02:55 24025518 reads; of these: 24025518 (100.00%) were unpaired; of these: 19731550 (82.13%) aligned 0 times 3059229 (12.73%) aligned exactly 1 time 1234739 (5.14%) aligned >1 times 17.87% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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_rmdupse_core] 2100356 / 4293968 = 0.4891 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 @ Thu, 16 Apr 2020 03:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.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, 16 Apr 2020 03:51:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:51:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:51:41: 1000000 INFO @ Thu, 16 Apr 2020 03:51:46: 2000000 INFO @ Thu, 16 Apr 2020 03:51:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:51:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:51:47: #1 total tags in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:51:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:51:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:51:47: #1 tags after filtering in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:51:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:51:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:51:47: #2 number of paired peaks: 137 WARNING @ Thu, 16 Apr 2020 03:51:47: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 16 Apr 2020 03:51:47: start model_add_line... INFO @ Thu, 16 Apr 2020 03:51:47: start X-correlation... INFO @ Thu, 16 Apr 2020 03:51:47: end of X-cor INFO @ Thu, 16 Apr 2020 03:51:47: #2 finished! INFO @ Thu, 16 Apr 2020 03:51:47: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:51:47: #2 alternative fragment length(s) may be 52,444 bps INFO @ Thu, 16 Apr 2020 03:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05_model.r WARNING @ Thu, 16 Apr 2020 03:51:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:51:47: #2 You may need to consider one of the other alternative d(s): 52,444 WARNING @ Thu, 16 Apr 2020 03:51:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:51:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:51:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.05_summits.bed INFO @ Thu, 16 Apr 2020 03:51:55: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 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 @ Thu, 16 Apr 2020 03:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.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, 16 Apr 2020 03:52:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:52:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:52:11: 1000000 INFO @ Thu, 16 Apr 2020 03:52:16: 2000000 INFO @ Thu, 16 Apr 2020 03:52:17: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:52:17: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:52:17: #1 total tags in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:52:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:52:17: #1 tags after filtering in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:52:17: #1 finished! INFO @ Thu, 16 Apr 2020 03:52:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:52:17: #2 number of paired peaks: 137 WARNING @ Thu, 16 Apr 2020 03:52:17: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 16 Apr 2020 03:52:17: start model_add_line... INFO @ Thu, 16 Apr 2020 03:52:17: start X-correlation... INFO @ Thu, 16 Apr 2020 03:52:17: end of X-cor INFO @ Thu, 16 Apr 2020 03:52:17: #2 finished! INFO @ Thu, 16 Apr 2020 03:52:17: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:52:17: #2 alternative fragment length(s) may be 52,444 bps INFO @ Thu, 16 Apr 2020 03:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10_model.r WARNING @ Thu, 16 Apr 2020 03:52:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:52:17: #2 You may need to consider one of the other alternative d(s): 52,444 WARNING @ Thu, 16 Apr 2020 03:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:52:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:52:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.10_summits.bed INFO @ Thu, 16 Apr 2020 03:52:24: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (165 records, 4 fields): 2 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 @ Thu, 16 Apr 2020 03:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.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, 16 Apr 2020 03:52:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:52:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:52:41: 1000000 INFO @ Thu, 16 Apr 2020 03:52:46: 2000000 INFO @ Thu, 16 Apr 2020 03:52:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:52:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:52:47: #1 total tags in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:52:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:52:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:52:47: #1 tags after filtering in treatment: 2193612 INFO @ Thu, 16 Apr 2020 03:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:52:47: #1 finished! INFO @ Thu, 16 Apr 2020 03:52:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:52:47: #2 number of paired peaks: 137 WARNING @ Thu, 16 Apr 2020 03:52:47: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 16 Apr 2020 03:52:47: start model_add_line... INFO @ Thu, 16 Apr 2020 03:52:47: start X-correlation... INFO @ Thu, 16 Apr 2020 03:52:47: end of X-cor INFO @ Thu, 16 Apr 2020 03:52:47: #2 finished! INFO @ Thu, 16 Apr 2020 03:52:47: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:52:47: #2 alternative fragment length(s) may be 52,444 bps INFO @ Thu, 16 Apr 2020 03:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20_model.r WARNING @ Thu, 16 Apr 2020 03:52:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:52:47: #2 You may need to consider one of the other alternative d(s): 52,444 WARNING @ Thu, 16 Apr 2020 03:52:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:52:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:52:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386766/SRX6386766.20_summits.bed INFO @ Thu, 16 Apr 2020 03:52:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (71 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。