Job ID = 5721178 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,448,173 reads read : 18,896,346 reads written : 18,896,346 2020-04-15T20:32:26 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 ) 2020-04-15T20:32:26 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 ) 2020-04-15T20:33:46 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 ) 2020-04-15T20:35:09 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 ) 2020-04-15T20:35:09 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 : 9,425,730 reads read : 18,851,460 reads written : 18,851,460 spots read : 9,189,501 reads read : 18,379,002 reads written : 18,379,002 spots read : 9,250,820 reads read : 18,501,640 reads written : 18,501,640 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: 00:07:13 37314224 reads; of these: 37314224 (100.00%) were paired; of these: 35744097 (95.79%) aligned concordantly 0 times 1185868 (3.18%) aligned concordantly exactly 1 time 384259 (1.03%) aligned concordantly >1 times ---- 35744097 pairs aligned concordantly 0 times; of these: 5870 (0.02%) aligned discordantly 1 time ---- 35738227 pairs aligned 0 times concordantly or discordantly; of these: 71476454 mates make up the pairs; of these: 70738316 (98.97%) aligned 0 times 150868 (0.21%) aligned exactly 1 time 587270 (0.82%) aligned >1 times 5.21% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 45308 / 1574528 = 0.0288 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 05:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.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 05:59:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:06: 1000000 INFO @ Thu, 16 Apr 2020 05:59:10: 2000000 INFO @ Thu, 16 Apr 2020 05:59:15: 3000000 INFO @ Thu, 16 Apr 2020 05:59:19: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:59:19: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:59:19: #1 total tags in treatment: 1524867 INFO @ Thu, 16 Apr 2020 05:59:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:19: #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 05:59:19: #1 tags after filtering in treatment: 1420347 INFO @ Thu, 16 Apr 2020 05:59:19: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:59:19: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:19: #2 number of paired peaks: 5538 INFO @ Thu, 16 Apr 2020 05:59:19: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:19: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:19: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:19: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:19: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 05:59:19: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 05:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05_model.r INFO @ Thu, 16 Apr 2020 05:59:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.05_summits.bed INFO @ Thu, 16 Apr 2020 05:59:24: Done! 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 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2572 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.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 05:59:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:36: 1000000 INFO @ Thu, 16 Apr 2020 05:59:41: 2000000 INFO @ Thu, 16 Apr 2020 05:59:46: 3000000 INFO @ Thu, 16 Apr 2020 05:59:50: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:59:50: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:59:50: #1 total tags in treatment: 1524867 INFO @ Thu, 16 Apr 2020 05:59:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:50: #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 05:59:50: #1 tags after filtering in treatment: 1420347 INFO @ Thu, 16 Apr 2020 05:59:50: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:59:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:50: #2 number of paired peaks: 5538 INFO @ Thu, 16 Apr 2020 05:59:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:50: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 05:59:50: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 05:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10_model.r INFO @ Thu, 16 Apr 2020 05:59:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.10_summits.bed INFO @ Thu, 16 Apr 2020 05:59:55: Done! 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 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.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 06:00:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:00:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:00:07: 1000000 INFO @ Thu, 16 Apr 2020 06:00:13: 2000000 INFO @ Thu, 16 Apr 2020 06:00:19: 3000000 INFO @ Thu, 16 Apr 2020 06:00:24: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:00:24: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:00:24: #1 total tags in treatment: 1524867 INFO @ Thu, 16 Apr 2020 06:00:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:00:24: #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 06:00:24: #1 tags after filtering in treatment: 1420347 INFO @ Thu, 16 Apr 2020 06:00:24: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:00:24: #1 finished! INFO @ Thu, 16 Apr 2020 06:00:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:00:24: #2 number of paired peaks: 5538 INFO @ Thu, 16 Apr 2020 06:00:24: start model_add_line... INFO @ Thu, 16 Apr 2020 06:00:24: start X-correlation... INFO @ Thu, 16 Apr 2020 06:00:24: end of X-cor INFO @ Thu, 16 Apr 2020 06:00:24: #2 finished! INFO @ Thu, 16 Apr 2020 06:00:24: #2 predicted fragment length is 169 bps INFO @ Thu, 16 Apr 2020 06:00:24: #2 alternative fragment length(s) may be 169 bps INFO @ Thu, 16 Apr 2020 06:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20_model.r INFO @ Thu, 16 Apr 2020 06:00:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:00:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762287/SRX6762287.20_summits.bed INFO @ Thu, 16 Apr 2020 06:00:29: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (292 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。