Job ID = 5720791 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:31:40 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 : 11,979,431 reads read : 23,958,862 reads written : 23,958,862 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: 00:33:12 11979431 reads; of these: 11979431 (100.00%) were paired; of these: 2425867 (20.25%) aligned concordantly 0 times 6968560 (58.17%) aligned concordantly exactly 1 time 2585004 (21.58%) aligned concordantly >1 times ---- 2425867 pairs aligned concordantly 0 times; of these: 860945 (35.49%) aligned discordantly 1 time ---- 1564922 pairs aligned 0 times concordantly or discordantly; of these: 3129844 mates make up the pairs; of these: 1607373 (51.36%) aligned 0 times 734541 (23.47%) aligned exactly 1 time 787930 (25.17%) aligned >1 times 93.29% overall alignment rate Time searching: 00:33:12 Overall time: 00:33:12 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 12 files... [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] 1583497 / 10022480 = 0.1580 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 02:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.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 02:19:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:19:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:19:39: 1000000 INFO @ Thu, 16 Apr 2020 02:19:45: 2000000 INFO @ Thu, 16 Apr 2020 02:19:51: 3000000 INFO @ Thu, 16 Apr 2020 02:19:57: 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 02:20:03: 5000000 INFO @ Thu, 16 Apr 2020 02:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.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 02:20:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:20:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:20:09: 6000000 INFO @ Thu, 16 Apr 2020 02:20:11: 1000000 INFO @ Thu, 16 Apr 2020 02:20:16: 7000000 INFO @ Thu, 16 Apr 2020 02:20:19: 2000000 INFO @ Thu, 16 Apr 2020 02:20:23: 8000000 INFO @ Thu, 16 Apr 2020 02:20:27: 3000000 INFO @ Thu, 16 Apr 2020 02:20:30: 9000000 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 02:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.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 02:20:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:20:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:20:35: 4000000 INFO @ Thu, 16 Apr 2020 02:20:37: 10000000 INFO @ Thu, 16 Apr 2020 02:20:42: 1000000 INFO @ Thu, 16 Apr 2020 02:20:43: 5000000 INFO @ Thu, 16 Apr 2020 02:20:44: 11000000 INFO @ Thu, 16 Apr 2020 02:20:49: 2000000 INFO @ Thu, 16 Apr 2020 02:20:51: 6000000 INFO @ Thu, 16 Apr 2020 02:20:51: 12000000 INFO @ Thu, 16 Apr 2020 02:20:55: 3000000 INFO @ Thu, 16 Apr 2020 02:20:58: 13000000 INFO @ Thu, 16 Apr 2020 02:20:58: 7000000 INFO @ Thu, 16 Apr 2020 02:21:02: 4000000 INFO @ Thu, 16 Apr 2020 02:21:05: 14000000 INFO @ Thu, 16 Apr 2020 02:21:06: 8000000 INFO @ Thu, 16 Apr 2020 02:21:09: 5000000 INFO @ Thu, 16 Apr 2020 02:21:12: 15000000 INFO @ Thu, 16 Apr 2020 02:21:14: 9000000 INFO @ Thu, 16 Apr 2020 02:21:16: 6000000 INFO @ Thu, 16 Apr 2020 02:21:19: 16000000 INFO @ Thu, 16 Apr 2020 02:21:22: 10000000 INFO @ Thu, 16 Apr 2020 02:21:23: 7000000 INFO @ Thu, 16 Apr 2020 02:21:26: 17000000 INFO @ Thu, 16 Apr 2020 02:21:29: 11000000 INFO @ Thu, 16 Apr 2020 02:21:30: 8000000 INFO @ Thu, 16 Apr 2020 02:21:33: 18000000 INFO @ Thu, 16 Apr 2020 02:21:37: 9000000 INFO @ Thu, 16 Apr 2020 02:21:37: 12000000 INFO @ Thu, 16 Apr 2020 02:21:40: 19000000 INFO @ Thu, 16 Apr 2020 02:21:41: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:21:41: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:21:41: #1 total tags in treatment: 8031668 INFO @ Thu, 16 Apr 2020 02:21:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:21:41: #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 02:21:41: #1 tags after filtering in treatment: 7686930 INFO @ Thu, 16 Apr 2020 02:21:41: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:21:41: #1 finished! INFO @ Thu, 16 Apr 2020 02:21:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:21:42: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 02:21:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 02:21:42: start model_add_line... INFO @ Thu, 16 Apr 2020 02:21:42: start X-correlation... INFO @ Thu, 16 Apr 2020 02:21:42: end of X-cor INFO @ Thu, 16 Apr 2020 02:21:42: #2 finished! INFO @ Thu, 16 Apr 2020 02:21:42: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 02:21:42: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 02:21:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05_model.r WARNING @ Thu, 16 Apr 2020 02:21:42: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:21:42: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Thu, 16 Apr 2020 02:21:42: #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 02:21:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:21:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:21:44: 10000000 INFO @ Thu, 16 Apr 2020 02:21:45: 13000000 INFO @ Thu, 16 Apr 2020 02:21:51: 11000000 INFO @ Thu, 16 Apr 2020 02:21:53: 14000000 INFO @ Thu, 16 Apr 2020 02:21:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:21:58: 12000000 INFO @ Thu, 16 Apr 2020 02:22:00: 15000000 INFO @ Thu, 16 Apr 2020 02:22:05: 13000000 INFO @ Thu, 16 Apr 2020 02:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.05_summits.bed INFO @ Thu, 16 Apr 2020 02:22:05: Done! INFO @ Thu, 16 Apr 2020 02:22:08: 16000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2081 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:22:12: 14000000 INFO @ Thu, 16 Apr 2020 02:22:16: 17000000 INFO @ Thu, 16 Apr 2020 02:22:20: 15000000 INFO @ Thu, 16 Apr 2020 02:22:24: 18000000 INFO @ Thu, 16 Apr 2020 02:22:27: 16000000 INFO @ Thu, 16 Apr 2020 02:22:31: 19000000 INFO @ Thu, 16 Apr 2020 02:22:33: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:22:33: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:22:33: #1 total tags in treatment: 8031668 INFO @ Thu, 16 Apr 2020 02:22:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:22:33: #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 02:22:33: #1 tags after filtering in treatment: 7686930 INFO @ Thu, 16 Apr 2020 02:22:33: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:22:33: #1 finished! INFO @ Thu, 16 Apr 2020 02:22:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:22:33: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 02:22:33: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 02:22:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:22:33: start X-correlation... INFO @ Thu, 16 Apr 2020 02:22:33: end of X-cor INFO @ Thu, 16 Apr 2020 02:22:33: #2 finished! INFO @ Thu, 16 Apr 2020 02:22:33: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 02:22:33: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 02:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10_model.r WARNING @ Thu, 16 Apr 2020 02:22:33: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:22:33: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Thu, 16 Apr 2020 02:22:33: #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 02:22:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:22:34: 17000000 INFO @ Thu, 16 Apr 2020 02:22:40: 18000000 INFO @ Thu, 16 Apr 2020 02:22:47: 19000000 INFO @ Thu, 16 Apr 2020 02:22:48: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:22:48: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:22:48: #1 total tags in treatment: 8031668 INFO @ Thu, 16 Apr 2020 02:22:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:22:48: #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 02:22:48: #1 tags after filtering in treatment: 7686930 INFO @ Thu, 16 Apr 2020 02:22:48: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 02:22:48: #1 finished! INFO @ Thu, 16 Apr 2020 02:22:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:22:48: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 02:22:48: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 02:22:48: start model_add_line... INFO @ Thu, 16 Apr 2020 02:22:48: start X-correlation... INFO @ Thu, 16 Apr 2020 02:22:48: end of X-cor INFO @ Thu, 16 Apr 2020 02:22:48: #2 finished! INFO @ Thu, 16 Apr 2020 02:22:48: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 02:22:48: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 02:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20_model.r WARNING @ Thu, 16 Apr 2020 02:22:48: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:22:48: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Thu, 16 Apr 2020 02:22:48: #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 02:22:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:22:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.10_summits.bed INFO @ Thu, 16 Apr 2020 02:22:57: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1287 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:23:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246883/SRX5246883.20_summits.bed INFO @ Thu, 16 Apr 2020 02:23:12: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (703 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。