Job ID = 5721171 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:25:47 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 ) 2020-04-15T20:25:47 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 : 9,863,675 reads read : 19,727,350 reads written : 19,727,350 2020-04-15T20:34:50 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 : 9,804,920 reads read : 19,609,840 reads written : 19,609,840 spots read : 9,639,838 reads read : 19,279,676 reads written : 19,279,676 spots read : 9,671,010 reads read : 19,342,020 reads written : 19,342,020 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: 00:07:10 38979443 reads; of these: 38979443 (100.00%) were paired; of these: 37595303 (96.45%) aligned concordantly 0 times 1055660 (2.71%) aligned concordantly exactly 1 time 328480 (0.84%) aligned concordantly >1 times ---- 37595303 pairs aligned concordantly 0 times; of these: 3157 (0.01%) aligned discordantly 1 time ---- 37592146 pairs aligned 0 times concordantly or discordantly; of these: 75184292 mates make up the pairs; of these: 74381614 (98.93%) aligned 0 times 162354 (0.22%) aligned exactly 1 time 640324 (0.85%) aligned >1 times 4.59% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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] 36547 / 1385641 = 0.0264 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 05:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.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 05:58:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:39: 1000000 INFO @ Thu, 16 Apr 2020 05:58:44: 2000000 INFO @ Thu, 16 Apr 2020 05:58:48: 3000000 INFO @ Thu, 16 Apr 2020 05:58:50: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:58:50: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:58:50: #1 total tags in treatment: 1347617 INFO @ Thu, 16 Apr 2020 05:58:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:58:50: #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 05:58:50: #1 tags after filtering in treatment: 1277185 INFO @ Thu, 16 Apr 2020 05:58:50: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:58:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:58:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:58:50: #2 number of paired peaks: 4425 INFO @ Thu, 16 Apr 2020 05:58:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:58:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:58:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:58:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:58:50: #2 predicted fragment length is 149 bps INFO @ Thu, 16 Apr 2020 05:58:50: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 16 Apr 2020 05:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05_model.r INFO @ Thu, 16 Apr 2020 05:58:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:58:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.05_summits.bed INFO @ Thu, 16 Apr 2020 05:58:55: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1373 records, 4 fields): 3 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 05:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.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 05:59:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:10: 1000000 INFO @ Thu, 16 Apr 2020 05:59:14: 2000000 INFO @ Thu, 16 Apr 2020 05:59:18: 3000000 INFO @ Thu, 16 Apr 2020 05:59:20: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 05:59:20: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 05:59:20: #1 total tags in treatment: 1347617 INFO @ Thu, 16 Apr 2020 05:59:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:20: #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 05:59:20: #1 tags after filtering in treatment: 1277185 INFO @ Thu, 16 Apr 2020 05:59:20: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:59:20: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:21: #2 number of paired peaks: 4425 INFO @ Thu, 16 Apr 2020 05:59:21: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:21: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:21: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:21: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:21: #2 predicted fragment length is 149 bps INFO @ Thu, 16 Apr 2020 05:59:21: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 16 Apr 2020 05:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10_model.r INFO @ Thu, 16 Apr 2020 05:59:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.10_summits.bed INFO @ Thu, 16 Apr 2020 05:59:25: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (452 records, 4 fields): 2 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 05:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.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 05:59:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:59:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:59:40: 1000000 INFO @ Thu, 16 Apr 2020 05:59:44: 2000000 INFO @ Thu, 16 Apr 2020 05:59:48: 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: 1347617 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: 1277185 INFO @ Thu, 16 Apr 2020 05:59:50: #1 Redundant rate of treatment: 0.05 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: 4425 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 149 bps INFO @ Thu, 16 Apr 2020 05:59:50: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 16 Apr 2020 05:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20_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 05:59:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762284/SRX6762284.20_summits.bed INFO @ Thu, 16 Apr 2020 05:59:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (203 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。