Job ID = 5721187 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,384,146 reads read : 6,768,292 reads written : 6,768,292 2020-04-15T20:34:38 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 ) 2020-04-15T20:34:38 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 : 3,344,684 reads read : 6,689,368 reads written : 6,689,368 spots read : 3,323,539 reads read : 6,647,078 reads written : 6,647,078 spots read : 3,319,071 reads read : 6,638,142 reads written : 6,638,142 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: 00:04:40 13371440 reads; of these: 13371440 (100.00%) were paired; of these: 11831580 (88.48%) aligned concordantly 0 times 1105736 (8.27%) aligned concordantly exactly 1 time 434124 (3.25%) aligned concordantly >1 times ---- 11831580 pairs aligned concordantly 0 times; of these: 6215 (0.05%) aligned discordantly 1 time ---- 11825365 pairs aligned 0 times concordantly or discordantly; of these: 23650730 mates make up the pairs; of these: 23159572 (97.92%) aligned 0 times 182792 (0.77%) aligned exactly 1 time 308366 (1.30%) aligned >1 times 13.40% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 30090 / 1541320 = 0.0195 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 05:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.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 05:47:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:47:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:47:40: 1000000 INFO @ Thu, 16 Apr 2020 05:47:44: 2000000 INFO @ Thu, 16 Apr 2020 05:47:49: 3000000 INFO @ Thu, 16 Apr 2020 05:47:51: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:47:51: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:47:51: #1 total tags in treatment: 1509804 INFO @ Thu, 16 Apr 2020 05:47:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:47:51: #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 05:47:51: #1 tags after filtering in treatment: 1469957 INFO @ Thu, 16 Apr 2020 05:47:51: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:47:51: #1 finished! INFO @ Thu, 16 Apr 2020 05:47:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:47:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:47:51: #2 number of paired peaks: 730 WARNING @ Thu, 16 Apr 2020 05:47:51: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Thu, 16 Apr 2020 05:47:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:47:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:47:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:47:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:47:51: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 05:47:51: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 05:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05_model.r INFO @ Thu, 16 Apr 2020 05:47:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:47:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.05_summits.bed INFO @ Thu, 16 Apr 2020 05:47:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (315 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 05:48:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.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 05:48:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:48:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:48:09: 1000000 INFO @ Thu, 16 Apr 2020 05:48:13: 2000000 INFO @ Thu, 16 Apr 2020 05:48:17: 3000000 INFO @ Thu, 16 Apr 2020 05:48:20: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:48:20: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:48:20: #1 total tags in treatment: 1509804 INFO @ Thu, 16 Apr 2020 05:48:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:48:20: #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 05:48:20: #1 tags after filtering in treatment: 1469957 INFO @ Thu, 16 Apr 2020 05:48:20: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:48:20: #1 finished! INFO @ Thu, 16 Apr 2020 05:48:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:48:20: #2 number of paired peaks: 730 WARNING @ Thu, 16 Apr 2020 05:48:20: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Thu, 16 Apr 2020 05:48:20: start model_add_line... INFO @ Thu, 16 Apr 2020 05:48:20: start X-correlation... INFO @ Thu, 16 Apr 2020 05:48:20: end of X-cor INFO @ Thu, 16 Apr 2020 05:48:20: #2 finished! INFO @ Thu, 16 Apr 2020 05:48:20: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 05:48:20: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 05:48:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10_model.r INFO @ Thu, 16 Apr 2020 05:48:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:48:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:48:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.10_summits.bed INFO @ Thu, 16 Apr 2020 05:48:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (119 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 05:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.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 05:48:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:48:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:48:40: 1000000 INFO @ Thu, 16 Apr 2020 05:48:44: 2000000 INFO @ Thu, 16 Apr 2020 05:48:48: 3000000 INFO @ Thu, 16 Apr 2020 05:48:50: #1 tag size is determined as 38 bps INFO @ Thu, 16 Apr 2020 05:48:50: #1 tag size = 38 INFO @ Thu, 16 Apr 2020 05:48:50: #1 total tags in treatment: 1509804 INFO @ Thu, 16 Apr 2020 05:48:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:48:50: #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 05:48:50: #1 tags after filtering in treatment: 1469957 INFO @ Thu, 16 Apr 2020 05:48:50: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:48:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:48:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:48:51: #2 number of paired peaks: 730 WARNING @ Thu, 16 Apr 2020 05:48:51: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Thu, 16 Apr 2020 05:48:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:48:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:48:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:48:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:48:51: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 05:48:51: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 05:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20_model.r INFO @ Thu, 16 Apr 2020 05:48:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:48:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762296/SRX6762296.20_summits.bed INFO @ Thu, 16 Apr 2020 05:48:55: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。