Job ID = 5720912 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:05:44 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 : 6,321,153 reads read : 12,642,306 reads written : 6,321,153 reads 0-length : 6,321,153 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: 00:01:19 6321153 reads; of these: 6321153 (100.00%) were unpaired; of these: 4868305 (77.02%) aligned 0 times 971578 (15.37%) aligned exactly 1 time 481270 (7.61%) aligned >1 times 22.98% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 247152 / 1452848 = 0.1701 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 03:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.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 03:10:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:10:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:10:27: 1000000 INFO @ Thu, 16 Apr 2020 03:10:28: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 03:10:28: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 03:10:28: #1 total tags in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:10:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:10:28: #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 03:10:28: #1 tags after filtering in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:10:28: #1 finished! INFO @ Thu, 16 Apr 2020 03:10:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:10:28: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 03:10:28: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 03:10:28: start model_add_line... INFO @ Thu, 16 Apr 2020 03:10:28: start X-correlation... INFO @ Thu, 16 Apr 2020 03:10:28: end of X-cor INFO @ Thu, 16 Apr 2020 03:10:28: #2 finished! INFO @ Thu, 16 Apr 2020 03:10:28: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:10:28: #2 alternative fragment length(s) may be 73,399,575 bps INFO @ Thu, 16 Apr 2020 03:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05_model.r WARNING @ Thu, 16 Apr 2020 03:10:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:10:28: #2 You may need to consider one of the other alternative d(s): 73,399,575 WARNING @ Thu, 16 Apr 2020 03:10:28: #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 03:10:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:10:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.05_summits.bed INFO @ Thu, 16 Apr 2020 03:10:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (485 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 03:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.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 03:10:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:10:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:10:54: 1000000 INFO @ Thu, 16 Apr 2020 03:10:55: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 03:10:55: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 03:10:55: #1 total tags in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:10:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:10:55: #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 03:10:55: #1 tags after filtering in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:10:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:10:55: #1 finished! INFO @ Thu, 16 Apr 2020 03:10:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:10:55: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 03:10:55: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 03:10:55: start model_add_line... INFO @ Thu, 16 Apr 2020 03:10:55: start X-correlation... INFO @ Thu, 16 Apr 2020 03:10:55: end of X-cor INFO @ Thu, 16 Apr 2020 03:10:55: #2 finished! INFO @ Thu, 16 Apr 2020 03:10:55: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:10:55: #2 alternative fragment length(s) may be 73,399,575 bps INFO @ Thu, 16 Apr 2020 03:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10_model.r WARNING @ Thu, 16 Apr 2020 03:10:55: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:10:55: #2 You may need to consider one of the other alternative d(s): 73,399,575 WARNING @ Thu, 16 Apr 2020 03:10:55: #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 03:10:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:10:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.10_summits.bed INFO @ Thu, 16 Apr 2020 03:10:59: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (216 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 @ Thu, 16 Apr 2020 03:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.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 03:11:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:11:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:11:24: 1000000 INFO @ Thu, 16 Apr 2020 03:11:25: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 03:11:25: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 03:11:25: #1 total tags in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:11:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:11:25: #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 03:11:25: #1 tags after filtering in treatment: 1205696 INFO @ Thu, 16 Apr 2020 03:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:11:25: #1 finished! INFO @ Thu, 16 Apr 2020 03:11:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:11:25: #2 number of paired peaks: 383 WARNING @ Thu, 16 Apr 2020 03:11:25: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 16 Apr 2020 03:11:25: start model_add_line... INFO @ Thu, 16 Apr 2020 03:11:25: start X-correlation... INFO @ Thu, 16 Apr 2020 03:11:25: end of X-cor INFO @ Thu, 16 Apr 2020 03:11:25: #2 finished! INFO @ Thu, 16 Apr 2020 03:11:25: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:11:25: #2 alternative fragment length(s) may be 73,399,575 bps INFO @ Thu, 16 Apr 2020 03:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20_model.r WARNING @ Thu, 16 Apr 2020 03:11:25: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:11:25: #2 You may need to consider one of the other alternative d(s): 73,399,575 WARNING @ Thu, 16 Apr 2020 03:11:25: #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 03:11:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:11:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 03:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775939/SRX5775939.20_summits.bed INFO @ Thu, 16 Apr 2020 03:11:29: Done! BigWig に変換しました。 pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 1 millis CompletedMACS2peakCalling