Job ID = 5720906 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:04:19 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 ) 2020-04-15T18:04:19 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 ) 2020-04-15T18:04:19 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 : 29,378,011 reads read : 29,378,011 reads written : 29,378,011 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: 00:08:32 29378011 reads; of these: 29378011 (100.00%) were unpaired; of these: 13921059 (47.39%) aligned 0 times 10930265 (37.21%) aligned exactly 1 time 4526687 (15.41%) aligned >1 times 52.61% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10407964 / 15456952 = 0.6734 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 03:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.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 03:28:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:28:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:28:53: 1000000 INFO @ Thu, 16 Apr 2020 03:28:59: 2000000 INFO @ Thu, 16 Apr 2020 03:29:05: 3000000 INFO @ Thu, 16 Apr 2020 03:29:11: 4000000 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 03:29:17: 5000000 INFO @ Thu, 16 Apr 2020 03:29:17: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:29:17: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:29:17: #1 total tags in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:29:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:29:17: #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 03:29:17: #1 tags after filtering in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:29:17: #1 finished! INFO @ Thu, 16 Apr 2020 03:29:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.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 03:29:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:18: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 03:29:18: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 03:29:18: start model_add_line... INFO @ Thu, 16 Apr 2020 03:29:18: start X-correlation... INFO @ Thu, 16 Apr 2020 03:29:18: end of X-cor INFO @ Thu, 16 Apr 2020 03:29:18: #2 finished! INFO @ Thu, 16 Apr 2020 03:29:18: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:29:18: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05_model.r WARNING @ Thu, 16 Apr 2020 03:29:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:29:18: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:29:18: #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 03:29:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:29:23: 1000000 INFO @ Thu, 16 Apr 2020 03:29:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:29:29: 2000000 INFO @ Thu, 16 Apr 2020 03:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.05_summits.bed INFO @ Thu, 16 Apr 2020 03:29:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3207 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:29:35: 3000000 INFO @ Thu, 16 Apr 2020 03:29:41: 4000000 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 03:29:47: 5000000 INFO @ Thu, 16 Apr 2020 03:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.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 03:29:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:48: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:29:48: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:29:48: #1 total tags in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:29:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:29:48: #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 03:29:48: #1 tags after filtering in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:29:48: #1 finished! INFO @ Thu, 16 Apr 2020 03:29:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:29:48: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 03:29:48: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 03:29:48: start model_add_line... INFO @ Thu, 16 Apr 2020 03:29:48: start X-correlation... INFO @ Thu, 16 Apr 2020 03:29:48: end of X-cor INFO @ Thu, 16 Apr 2020 03:29:48: #2 finished! INFO @ Thu, 16 Apr 2020 03:29:48: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:29:48: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10_model.r WARNING @ Thu, 16 Apr 2020 03:29:48: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:29:48: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:29:48: #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 03:29:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:29:53: 1000000 INFO @ Thu, 16 Apr 2020 03:29:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:30:00: 2000000 INFO @ Thu, 16 Apr 2020 03:30:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:30:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:30:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.10_summits.bed INFO @ Thu, 16 Apr 2020 03:30:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:30:06: 3000000 INFO @ Thu, 16 Apr 2020 03:30:12: 4000000 INFO @ Thu, 16 Apr 2020 03:30:18: 5000000 INFO @ Thu, 16 Apr 2020 03:30:18: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:30:18: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:30:18: #1 total tags in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:30:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:30:18: #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 03:30:18: #1 tags after filtering in treatment: 5048988 INFO @ Thu, 16 Apr 2020 03:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:30:18: #1 finished! INFO @ Thu, 16 Apr 2020 03:30:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:30:18: #2 number of paired peaks: 848 WARNING @ Thu, 16 Apr 2020 03:30:18: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Thu, 16 Apr 2020 03:30:18: start model_add_line... INFO @ Thu, 16 Apr 2020 03:30:18: start X-correlation... INFO @ Thu, 16 Apr 2020 03:30:18: end of X-cor INFO @ Thu, 16 Apr 2020 03:30:18: #2 finished! INFO @ Thu, 16 Apr 2020 03:30:18: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:30:18: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20_model.r WARNING @ Thu, 16 Apr 2020 03:30:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:30:18: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:30:18: #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 03:30:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:30:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:30:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775933/SRX5775933.20_summits.bed INFO @ Thu, 16 Apr 2020 03:30:35: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (580 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。