Job ID = 5721186 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,337,308 reads read : 6,674,616 reads written : 6,674,616 spots read : 3,305,224 reads read : 6,610,448 reads written : 6,610,448 2020-04-15T20:36:29 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 ) 2020-04-15T20:36:29 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 : 3,264,335 reads read : 6,528,670 reads written : 6,528,670 spots read : 3,265,591 reads read : 6,531,182 reads written : 6,531,182 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: 00:02:48 13172458 reads; of these: 13172458 (100.00%) were paired; of these: 12657184 (96.09%) aligned concordantly 0 times 356016 (2.70%) aligned concordantly exactly 1 time 159258 (1.21%) aligned concordantly >1 times ---- 12657184 pairs aligned concordantly 0 times; of these: 1227 (0.01%) aligned discordantly 1 time ---- 12655957 pairs aligned 0 times concordantly or discordantly; of these: 25311914 mates make up the pairs; of these: 25035597 (98.91%) aligned 0 times 53475 (0.21%) aligned exactly 1 time 222842 (0.88%) aligned >1 times 4.97% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 9335 / 515869 = 0.0181 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 05:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.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 05:44:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:44:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:44:44: 1000000 INFO @ Thu, 16 Apr 2020 05:44:45: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:44:45: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:44:45: #1 total tags in treatment: 505951 INFO @ Thu, 16 Apr 2020 05:44:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:44:45: #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 05:44:45: #1 tags after filtering in treatment: 496493 INFO @ Thu, 16 Apr 2020 05:44:45: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:44:45: #1 finished! INFO @ Thu, 16 Apr 2020 05:44:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:44:45: #2 number of paired peaks: 979 WARNING @ Thu, 16 Apr 2020 05:44:45: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Thu, 16 Apr 2020 05:44:45: start model_add_line... INFO @ Thu, 16 Apr 2020 05:44:45: start X-correlation... INFO @ Thu, 16 Apr 2020 05:44:45: end of X-cor INFO @ Thu, 16 Apr 2020 05:44:45: #2 finished! INFO @ Thu, 16 Apr 2020 05:44:45: #2 predicted fragment length is 87 bps INFO @ Thu, 16 Apr 2020 05:44:45: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 16 Apr 2020 05:44:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05_model.r INFO @ Thu, 16 Apr 2020 05:44:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:44:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:44:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.05_summits.bed INFO @ Thu, 16 Apr 2020 05:44:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (104 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 05:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.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 05:45:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:45:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:45:15: 1000000 INFO @ Thu, 16 Apr 2020 05:45:16: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:45:16: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:45:16: #1 total tags in treatment: 505951 INFO @ Thu, 16 Apr 2020 05:45:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:45:16: #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 05:45:16: #1 tags after filtering in treatment: 496493 INFO @ Thu, 16 Apr 2020 05:45:16: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:45:16: #1 finished! INFO @ Thu, 16 Apr 2020 05:45:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:45:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:45:16: #2 number of paired peaks: 979 WARNING @ Thu, 16 Apr 2020 05:45:16: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Thu, 16 Apr 2020 05:45:16: start model_add_line... INFO @ Thu, 16 Apr 2020 05:45:16: start X-correlation... INFO @ Thu, 16 Apr 2020 05:45:16: end of X-cor INFO @ Thu, 16 Apr 2020 05:45:16: #2 finished! INFO @ Thu, 16 Apr 2020 05:45:16: #2 predicted fragment length is 87 bps INFO @ Thu, 16 Apr 2020 05:45:16: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 16 Apr 2020 05:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10_model.r INFO @ Thu, 16 Apr 2020 05:45:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:45:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.10_summits.bed INFO @ Thu, 16 Apr 2020 05:45:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (60 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 05:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.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 05:45:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:45:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:45:45: 1000000 INFO @ Thu, 16 Apr 2020 05:45:46: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:45:46: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:45:46: #1 total tags in treatment: 505951 INFO @ Thu, 16 Apr 2020 05:45:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:45:46: #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 05:45:46: #1 tags after filtering in treatment: 496493 INFO @ Thu, 16 Apr 2020 05:45:46: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:45:46: #1 finished! INFO @ Thu, 16 Apr 2020 05:45:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:45:46: #2 number of paired peaks: 979 WARNING @ Thu, 16 Apr 2020 05:45:46: Fewer paired peaks (979) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 979 pairs to build model! INFO @ Thu, 16 Apr 2020 05:45:46: start model_add_line... INFO @ Thu, 16 Apr 2020 05:45:46: start X-correlation... INFO @ Thu, 16 Apr 2020 05:45:46: end of X-cor INFO @ Thu, 16 Apr 2020 05:45:46: #2 finished! INFO @ Thu, 16 Apr 2020 05:45:46: #2 predicted fragment length is 87 bps INFO @ Thu, 16 Apr 2020 05:45:46: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 16 Apr 2020 05:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20_model.r INFO @ Thu, 16 Apr 2020 05:45:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:45:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:45:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762295/SRX6762295.20_summits.bed INFO @ Thu, 16 Apr 2020 05:45:48: Done! BigWig に変換しました。 pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 0 millis CompletedMACS2peakCalling