Job ID = 5720719 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:01:53 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 : 12,448,917 reads read : 12,448,917 reads written : 12,448,917 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: 00:03:00 12448917 reads; of these: 12448917 (100.00%) were unpaired; of these: 526147 (4.23%) aligned 0 times 10416599 (83.67%) aligned exactly 1 time 1506171 (12.10%) aligned >1 times 95.77% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 2736098 / 11922770 = 0.2295 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 01:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.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 01:14:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:14:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:14:47: 1000000 INFO @ Thu, 16 Apr 2020 01:14:52: 2000000 INFO @ Thu, 16 Apr 2020 01:14:58: 3000000 INFO @ Thu, 16 Apr 2020 01:15:04: 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 01:15:10: 5000000 INFO @ Thu, 16 Apr 2020 01:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.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 01:15:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:16: 6000000 INFO @ Thu, 16 Apr 2020 01:15:17: 1000000 INFO @ Thu, 16 Apr 2020 01:15:22: 7000000 INFO @ Thu, 16 Apr 2020 01:15:22: 2000000 INFO @ Thu, 16 Apr 2020 01:15:27: 8000000 INFO @ Thu, 16 Apr 2020 01:15:28: 3000000 INFO @ Thu, 16 Apr 2020 01:15:33: 9000000 INFO @ Thu, 16 Apr 2020 01:15:34: 4000000 INFO @ Thu, 16 Apr 2020 01:15:35: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:15:35: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:15:35: #1 total tags in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:15:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:15:35: #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 01:15:35: #1 tags after filtering in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:15:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:15:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:15:36: #2 number of paired peaks: 4296 INFO @ Thu, 16 Apr 2020 01:15:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:15:36: start X-correlation... INFO @ Thu, 16 Apr 2020 01:15:36: end of X-cor INFO @ Thu, 16 Apr 2020 01:15:36: #2 finished! INFO @ Thu, 16 Apr 2020 01:15:36: #2 predicted fragment length is 142 bps INFO @ Thu, 16 Apr 2020 01:15:36: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 16 Apr 2020 01:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05_model.r INFO @ Thu, 16 Apr 2020 01:15:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:15:39: 5000000 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 01:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.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 01:15:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:44: 6000000 INFO @ Thu, 16 Apr 2020 01:15:47: 1000000 INFO @ Thu, 16 Apr 2020 01:15:50: 7000000 INFO @ Thu, 16 Apr 2020 01:15:53: 2000000 INFO @ Thu, 16 Apr 2020 01:15:55: 8000000 INFO @ Thu, 16 Apr 2020 01:15:58: 3000000 INFO @ Thu, 16 Apr 2020 01:16:01: 9000000 INFO @ Thu, 16 Apr 2020 01:16:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:16:02: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:16:02: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:16:02: #1 total tags in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:16:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:16:02: #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 01:16:02: #1 tags after filtering in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:16:02: #1 finished! INFO @ Thu, 16 Apr 2020 01:16:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:16:03: #2 number of paired peaks: 4296 INFO @ Thu, 16 Apr 2020 01:16:03: start model_add_line... INFO @ Thu, 16 Apr 2020 01:16:03: start X-correlation... INFO @ Thu, 16 Apr 2020 01:16:03: end of X-cor INFO @ Thu, 16 Apr 2020 01:16:03: #2 finished! INFO @ Thu, 16 Apr 2020 01:16:03: #2 predicted fragment length is 142 bps INFO @ Thu, 16 Apr 2020 01:16:03: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 16 Apr 2020 01:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10_model.r INFO @ Thu, 16 Apr 2020 01:16:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:16:04: 4000000 INFO @ Thu, 16 Apr 2020 01:16:09: 5000000 INFO @ Thu, 16 Apr 2020 01:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.05_summits.bed INFO @ Thu, 16 Apr 2020 01:16:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5117 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:16:15: 6000000 INFO @ Thu, 16 Apr 2020 01:16:20: 7000000 INFO @ Thu, 16 Apr 2020 01:16:25: 8000000 INFO @ Thu, 16 Apr 2020 01:16:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:16:31: 9000000 INFO @ Thu, 16 Apr 2020 01:16:32: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:16:32: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:16:32: #1 total tags in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:16:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:16:32: #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 01:16:32: #1 tags after filtering in treatment: 9186672 INFO @ Thu, 16 Apr 2020 01:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:16:32: #1 finished! INFO @ Thu, 16 Apr 2020 01:16:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:16:33: #2 number of paired peaks: 4296 INFO @ Thu, 16 Apr 2020 01:16:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:16:33: start X-correlation... INFO @ Thu, 16 Apr 2020 01:16:33: end of X-cor INFO @ Thu, 16 Apr 2020 01:16:33: #2 finished! INFO @ Thu, 16 Apr 2020 01:16:33: #2 predicted fragment length is 142 bps INFO @ Thu, 16 Apr 2020 01:16:33: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 16 Apr 2020 01:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20_model.r INFO @ Thu, 16 Apr 2020 01:16:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.10_summits.bed INFO @ Thu, 16 Apr 2020 01:16:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3891 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:16:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:17:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:17:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:17:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158183/SRX4158183.20_summits.bed INFO @ Thu, 16 Apr 2020 01:17:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2752 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。