Job ID = 5721123 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:00:53 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 ) 2020-04-15T20:00:53 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 : 6,081,218 reads read : 12,162,436 reads written : 12,162,436 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: 00:14:38 6081218 reads; of these: 6081218 (100.00%) were paired; of these: 710134 (11.68%) aligned concordantly 0 times 3753455 (61.72%) aligned concordantly exactly 1 time 1617629 (26.60%) aligned concordantly >1 times ---- 710134 pairs aligned concordantly 0 times; of these: 226431 (31.89%) aligned discordantly 1 time ---- 483703 pairs aligned 0 times concordantly or discordantly; of these: 967406 mates make up the pairs; of these: 590362 (61.03%) aligned 0 times 166894 (17.25%) aligned exactly 1 time 210150 (21.72%) aligned >1 times 95.15% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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_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] 296660 / 5543612 = 0.0535 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 05:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.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 05:21:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:09: 1000000 INFO @ Thu, 16 Apr 2020 05:21:15: 2000000 INFO @ Thu, 16 Apr 2020 05:21:21: 3000000 INFO @ Thu, 16 Apr 2020 05:21:27: 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 05:21:33: 5000000 INFO @ Thu, 16 Apr 2020 05:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.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 05:21:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:40: 6000000 INFO @ Thu, 16 Apr 2020 05:21:41: 1000000 INFO @ Thu, 16 Apr 2020 05:21:48: 7000000 INFO @ Thu, 16 Apr 2020 05:21:49: 2000000 INFO @ Thu, 16 Apr 2020 05:21:55: 8000000 INFO @ Thu, 16 Apr 2020 05:21:56: 3000000 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 05:22:02: 9000000 INFO @ Thu, 16 Apr 2020 05:22:03: 4000000 INFO @ Thu, 16 Apr 2020 05:22:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.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 05:22:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:22:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:22:09: 10000000 INFO @ Thu, 16 Apr 2020 05:22:10: 5000000 INFO @ Thu, 16 Apr 2020 05:22:11: 1000000 INFO @ Thu, 16 Apr 2020 05:22:16: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:16: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:16: #1 total tags in treatment: 5079004 INFO @ Thu, 16 Apr 2020 05:22:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:16: #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 05:22:16: #1 tags after filtering in treatment: 4903650 INFO @ Thu, 16 Apr 2020 05:22:16: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:16: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:17: #2 number of paired peaks: 1073 INFO @ Thu, 16 Apr 2020 05:22:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:17: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 05:22:17: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 05:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05_model.r WARNING @ Thu, 16 Apr 2020 05:22:17: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:22:17: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Thu, 16 Apr 2020 05:22:17: #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 05:22:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:17: 6000000 INFO @ Thu, 16 Apr 2020 05:22:18: 2000000 INFO @ Thu, 16 Apr 2020 05:22:24: 7000000 INFO @ Thu, 16 Apr 2020 05:22:25: 3000000 INFO @ Thu, 16 Apr 2020 05:22:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:31: 8000000 INFO @ Thu, 16 Apr 2020 05:22:32: 4000000 INFO @ Thu, 16 Apr 2020 05:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.05_summits.bed INFO @ Thu, 16 Apr 2020 05:22:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1513 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:22:38: 9000000 INFO @ Thu, 16 Apr 2020 05:22:39: 5000000 INFO @ Thu, 16 Apr 2020 05:22:45: 10000000 INFO @ Thu, 16 Apr 2020 05:22:46: 6000000 INFO @ Thu, 16 Apr 2020 05:22:52: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:52: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:52: #1 total tags in treatment: 5079004 INFO @ Thu, 16 Apr 2020 05:22:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:52: #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 05:22:52: #1 tags after filtering in treatment: 4903650 INFO @ Thu, 16 Apr 2020 05:22:52: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:52: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:52: #2 number of paired peaks: 1073 INFO @ Thu, 16 Apr 2020 05:22:52: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:52: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:52: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:52: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:52: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 05:22:52: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 05:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10_model.r WARNING @ Thu, 16 Apr 2020 05:22:52: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:22:52: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Thu, 16 Apr 2020 05:22:52: #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 05:22:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:52: 7000000 INFO @ Thu, 16 Apr 2020 05:22:59: 8000000 INFO @ Thu, 16 Apr 2020 05:23:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:05: 9000000 INFO @ Thu, 16 Apr 2020 05:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.10_summits.bed INFO @ Thu, 16 Apr 2020 05:23:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:23:11: 10000000 INFO @ Thu, 16 Apr 2020 05:23:17: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:23:17: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:23:17: #1 total tags in treatment: 5079004 INFO @ Thu, 16 Apr 2020 05:23:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:23:17: #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 05:23:17: #1 tags after filtering in treatment: 4903650 INFO @ Thu, 16 Apr 2020 05:23:17: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:23:17: #1 finished! INFO @ Thu, 16 Apr 2020 05:23:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:23:17: #2 number of paired peaks: 1073 INFO @ Thu, 16 Apr 2020 05:23:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:23:18: start X-correlation... INFO @ Thu, 16 Apr 2020 05:23:18: end of X-cor INFO @ Thu, 16 Apr 2020 05:23:18: #2 finished! INFO @ Thu, 16 Apr 2020 05:23:18: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 05:23:18: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 05:23:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20_model.r WARNING @ Thu, 16 Apr 2020 05:23:18: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:23:18: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Thu, 16 Apr 2020 05:23:18: #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 05:23:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:23:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708265/SRX6708265.20_summits.bed INFO @ Thu, 16 Apr 2020 05:23:34: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (449 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。