Job ID = 5720716 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 : 12,816,499 reads read : 12,816,499 reads written : 12,816,499 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: 00:02:42 12816499 reads; of these: 12816499 (100.00%) were unpaired; of these: 242302 (1.89%) aligned 0 times 11429999 (89.18%) aligned exactly 1 time 1144198 (8.93%) aligned >1 times 98.11% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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_rmdupse_core] 1634513 / 12574197 = 0.1300 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 01:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.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 01:15:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:41: 1000000 INFO @ Thu, 16 Apr 2020 01:15:47: 2000000 INFO @ Thu, 16 Apr 2020 01:15:53: 3000000 INFO @ Thu, 16 Apr 2020 01:15:59: 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 01:16:04: 5000000 INFO @ Thu, 16 Apr 2020 01:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.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 01:16:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:16:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:16:11: 6000000 INFO @ Thu, 16 Apr 2020 01:16:12: 1000000 INFO @ Thu, 16 Apr 2020 01:16:17: 7000000 INFO @ Thu, 16 Apr 2020 01:16:18: 2000000 INFO @ Thu, 16 Apr 2020 01:16:24: 8000000 INFO @ Thu, 16 Apr 2020 01:16:24: 3000000 INFO @ Thu, 16 Apr 2020 01:16:30: 9000000 INFO @ Thu, 16 Apr 2020 01:16:31: 4000000 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 01:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.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 01:16:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:16:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:16:36: 10000000 INFO @ Thu, 16 Apr 2020 01:16:37: 5000000 INFO @ Thu, 16 Apr 2020 01:16:42: 1000000 INFO @ Thu, 16 Apr 2020 01:16:42: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:16:42: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:16:42: #1 total tags in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:16:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:16:42: #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 01:16:42: #1 tags after filtering in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:16:42: #1 finished! INFO @ Thu, 16 Apr 2020 01:16:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:16:44: 6000000 INFO @ Thu, 16 Apr 2020 01:16:44: #2 number of paired peaks: 9259 INFO @ Thu, 16 Apr 2020 01:16:44: start model_add_line... INFO @ Thu, 16 Apr 2020 01:16:44: start X-correlation... INFO @ Thu, 16 Apr 2020 01:16:44: end of X-cor INFO @ Thu, 16 Apr 2020 01:16:44: #2 finished! INFO @ Thu, 16 Apr 2020 01:16:44: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 01:16:44: #2 alternative fragment length(s) may be 3,133 bps INFO @ Thu, 16 Apr 2020 01:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05_model.r INFO @ Thu, 16 Apr 2020 01:16:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:16:48: 2000000 INFO @ Thu, 16 Apr 2020 01:16:50: 7000000 INFO @ Thu, 16 Apr 2020 01:16:54: 3000000 INFO @ Thu, 16 Apr 2020 01:16:57: 8000000 INFO @ Thu, 16 Apr 2020 01:17:01: 4000000 INFO @ Thu, 16 Apr 2020 01:17:03: 9000000 INFO @ Thu, 16 Apr 2020 01:17:07: 5000000 INFO @ Thu, 16 Apr 2020 01:17:10: 10000000 INFO @ Thu, 16 Apr 2020 01:17:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:17:13: 6000000 INFO @ Thu, 16 Apr 2020 01:17:16: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:17:16: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:17:16: #1 total tags in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:17:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:17:16: #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 01:17:16: #1 tags after filtering in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:17:16: #1 finished! INFO @ Thu, 16 Apr 2020 01:17:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:17:17: #2 number of paired peaks: 9259 INFO @ Thu, 16 Apr 2020 01:17:17: start model_add_line... INFO @ Thu, 16 Apr 2020 01:17:17: start X-correlation... INFO @ Thu, 16 Apr 2020 01:17:17: end of X-cor INFO @ Thu, 16 Apr 2020 01:17:17: #2 finished! INFO @ Thu, 16 Apr 2020 01:17:17: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 01:17:17: #2 alternative fragment length(s) may be 3,133 bps INFO @ Thu, 16 Apr 2020 01:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10_model.r INFO @ Thu, 16 Apr 2020 01:17:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:17:20: 7000000 INFO @ Thu, 16 Apr 2020 01:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.05_summits.bed INFO @ Thu, 16 Apr 2020 01:17:25: Done! INFO @ Thu, 16 Apr 2020 01:17:26: 8000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9663 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:17:32: 9000000 INFO @ Thu, 16 Apr 2020 01:17:38: 10000000 INFO @ Thu, 16 Apr 2020 01:17:43: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:17:43: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:17:43: #1 total tags in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:17:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:17:43: #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 01:17:43: #1 tags after filtering in treatment: 10939684 INFO @ Thu, 16 Apr 2020 01:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:17:43: #1 finished! INFO @ Thu, 16 Apr 2020 01:17:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:17:44: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:17:45: #2 number of paired peaks: 9259 INFO @ Thu, 16 Apr 2020 01:17:45: start model_add_line... INFO @ Thu, 16 Apr 2020 01:17:45: start X-correlation... INFO @ Thu, 16 Apr 2020 01:17:45: end of X-cor INFO @ Thu, 16 Apr 2020 01:17:45: #2 finished! INFO @ Thu, 16 Apr 2020 01:17:45: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 01:17:45: #2 alternative fragment length(s) may be 3,133 bps INFO @ Thu, 16 Apr 2020 01:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20_model.r INFO @ Thu, 16 Apr 2020 01:17:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.10_summits.bed INFO @ Thu, 16 Apr 2020 01:17:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5199 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:18:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158180/SRX4158180.20_summits.bed INFO @ Thu, 16 Apr 2020 01:18:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1545 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。