Job ID = 5720806 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:30:52 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 ) 2020-04-15T16:30:52 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 ) 2020-04-15T16:30:52 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 : 13,798,366 reads read : 27,596,732 reads written : 27,596,732 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: 00:36:32 13798366 reads; of these: 13798366 (100.00%) were paired; of these: 2662769 (19.30%) aligned concordantly 0 times 9991421 (72.41%) aligned concordantly exactly 1 time 1144176 (8.29%) aligned concordantly >1 times ---- 2662769 pairs aligned concordantly 0 times; of these: 23737 (0.89%) aligned discordantly 1 time ---- 2639032 pairs aligned 0 times concordantly or discordantly; of these: 5278064 mates make up the pairs; of these: 4016366 (76.10%) aligned 0 times 413018 (7.83%) aligned exactly 1 time 848680 (16.08%) aligned >1 times 85.45% overall alignment rate Time searching: 00:36:32 Overall time: 00:36:32 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 12 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] 4738806 / 11143746 = 0.4252 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 02:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.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 02:26:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:26:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:26:23: 1000000 INFO @ Thu, 16 Apr 2020 02:26:30: 2000000 INFO @ Thu, 16 Apr 2020 02:26:37: 3000000 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 02:26:44: 4000000 INFO @ Thu, 16 Apr 2020 02:26:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.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 02:26:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:26:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:26:52: 5000000 INFO @ Thu, 16 Apr 2020 02:26:53: 1000000 INFO @ Thu, 16 Apr 2020 02:27:01: 6000000 INFO @ Thu, 16 Apr 2020 02:27:02: 2000000 INFO @ Thu, 16 Apr 2020 02:27:09: 7000000 INFO @ Thu, 16 Apr 2020 02:27:11: 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 02:27:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.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 02:27:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:27:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:27:18: 8000000 INFO @ Thu, 16 Apr 2020 02:27:20: 4000000 INFO @ Thu, 16 Apr 2020 02:27:23: 1000000 INFO @ Thu, 16 Apr 2020 02:27:26: 9000000 INFO @ Thu, 16 Apr 2020 02:27:28: 5000000 INFO @ Thu, 16 Apr 2020 02:27:32: 2000000 INFO @ Thu, 16 Apr 2020 02:27:35: 10000000 INFO @ Thu, 16 Apr 2020 02:27:36: 6000000 INFO @ Thu, 16 Apr 2020 02:27:41: 3000000 INFO @ Thu, 16 Apr 2020 02:27:43: 11000000 INFO @ Thu, 16 Apr 2020 02:27:44: 7000000 INFO @ Thu, 16 Apr 2020 02:27:50: 4000000 INFO @ Thu, 16 Apr 2020 02:27:52: 12000000 INFO @ Thu, 16 Apr 2020 02:27:52: 8000000 INFO @ Thu, 16 Apr 2020 02:27:58: 5000000 INFO @ Thu, 16 Apr 2020 02:28:00: 9000000 INFO @ Thu, 16 Apr 2020 02:28:00: 13000000 INFO @ Thu, 16 Apr 2020 02:28:06: 6000000 INFO @ Thu, 16 Apr 2020 02:28:08: 10000000 INFO @ Thu, 16 Apr 2020 02:28:08: 14000000 INFO @ Thu, 16 Apr 2020 02:28:09: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:28:09: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:28:09: #1 total tags in treatment: 6402027 INFO @ Thu, 16 Apr 2020 02:28:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:28:09: #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 02:28:09: #1 tags after filtering in treatment: 5393137 INFO @ Thu, 16 Apr 2020 02:28:09: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:28:09: #1 finished! INFO @ Thu, 16 Apr 2020 02:28:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:28:10: #2 number of paired peaks: 5813 INFO @ Thu, 16 Apr 2020 02:28:10: start model_add_line... INFO @ Thu, 16 Apr 2020 02:28:10: start X-correlation... INFO @ Thu, 16 Apr 2020 02:28:10: end of X-cor INFO @ Thu, 16 Apr 2020 02:28:10: #2 finished! INFO @ Thu, 16 Apr 2020 02:28:10: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:28:10: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05_model.r INFO @ Thu, 16 Apr 2020 02:28:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:28:14: 7000000 INFO @ Thu, 16 Apr 2020 02:28:15: 11000000 INFO @ Thu, 16 Apr 2020 02:28:22: 8000000 INFO @ Thu, 16 Apr 2020 02:28:23: 12000000 INFO @ Thu, 16 Apr 2020 02:28:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:28:30: 9000000 INFO @ Thu, 16 Apr 2020 02:28:30: 13000000 INFO @ Thu, 16 Apr 2020 02:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.05_summits.bed INFO @ Thu, 16 Apr 2020 02:28:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7134 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:28:37: 10000000 INFO @ Thu, 16 Apr 2020 02:28:38: 14000000 INFO @ Thu, 16 Apr 2020 02:28:38: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:28:38: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:28:38: #1 total tags in treatment: 6402027 INFO @ Thu, 16 Apr 2020 02:28:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:28:38: #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 02:28:39: #1 tags after filtering in treatment: 5393137 INFO @ Thu, 16 Apr 2020 02:28:39: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:28:39: #1 finished! INFO @ Thu, 16 Apr 2020 02:28:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:28:39: #2 number of paired peaks: 5813 INFO @ Thu, 16 Apr 2020 02:28:39: start model_add_line... INFO @ Thu, 16 Apr 2020 02:28:39: start X-correlation... INFO @ Thu, 16 Apr 2020 02:28:39: end of X-cor INFO @ Thu, 16 Apr 2020 02:28:39: #2 finished! INFO @ Thu, 16 Apr 2020 02:28:39: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:28:39: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10_model.r INFO @ Thu, 16 Apr 2020 02:28:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:28:44: 11000000 INFO @ Thu, 16 Apr 2020 02:28:51: 12000000 INFO @ Thu, 16 Apr 2020 02:28:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:28:58: 13000000 INFO @ Thu, 16 Apr 2020 02:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.10_summits.bed INFO @ Thu, 16 Apr 2020 02:29:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5796 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:29:05: 14000000 INFO @ Thu, 16 Apr 2020 02:29:05: #1 tag size is determined as 78 bps INFO @ Thu, 16 Apr 2020 02:29:05: #1 tag size = 78 INFO @ Thu, 16 Apr 2020 02:29:05: #1 total tags in treatment: 6402027 INFO @ Thu, 16 Apr 2020 02:29:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:29:05: #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 02:29:05: #1 tags after filtering in treatment: 5393137 INFO @ Thu, 16 Apr 2020 02:29:05: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 02:29:05: #1 finished! INFO @ Thu, 16 Apr 2020 02:29:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:29:06: #2 number of paired peaks: 5813 INFO @ Thu, 16 Apr 2020 02:29:06: start model_add_line... INFO @ Thu, 16 Apr 2020 02:29:06: start X-correlation... INFO @ Thu, 16 Apr 2020 02:29:06: end of X-cor INFO @ Thu, 16 Apr 2020 02:29:06: #2 finished! INFO @ Thu, 16 Apr 2020 02:29:06: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 02:29:06: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 02:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20_model.r INFO @ Thu, 16 Apr 2020 02:29:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:29:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 02:29:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309716/SRX5309716.20_summits.bed INFO @ Thu, 16 Apr 2020 02:29:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4519 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。