Job ID = 5720809 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:38:31 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 ) 2020-04-15T16:38:31 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 ) 2020-04-15T16:38:31 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 ) 2020-04-15T16:40:59 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 : 15,106,324 reads read : 30,212,648 reads written : 30,212,648 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: 00:20:14 15106324 reads; of these: 15106324 (100.00%) were paired; of these: 6501790 (43.04%) aligned concordantly 0 times 6718138 (44.47%) aligned concordantly exactly 1 time 1886396 (12.49%) aligned concordantly >1 times ---- 6501790 pairs aligned concordantly 0 times; of these: 16330 (0.25%) aligned discordantly 1 time ---- 6485460 pairs aligned 0 times concordantly or discordantly; of these: 12970920 mates make up the pairs; of these: 12373580 (95.39%) aligned 0 times 249957 (1.93%) aligned exactly 1 time 347383 (2.68%) aligned >1 times 59.05% overall alignment rate Time searching: 00:20:14 Overall time: 00:20:14 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_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] 2992068 / 8608604 = 0.3476 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 02:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.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 02:09:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:09:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:10:00: 1000000 INFO @ Thu, 16 Apr 2020 02:10:06: 2000000 INFO @ Thu, 16 Apr 2020 02:10:12: 3000000 INFO @ Thu, 16 Apr 2020 02:10:17: 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 02:10:23: 5000000 INFO @ Thu, 16 Apr 2020 02:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.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 02:10:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:10:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:10:30: 6000000 INFO @ Thu, 16 Apr 2020 02:10:31: 1000000 INFO @ Thu, 16 Apr 2020 02:10:36: 7000000 INFO @ Thu, 16 Apr 2020 02:10:37: 2000000 INFO @ Thu, 16 Apr 2020 02:10:43: 8000000 INFO @ Thu, 16 Apr 2020 02:10:44: 3000000 INFO @ Thu, 16 Apr 2020 02:10:49: 9000000 INFO @ Thu, 16 Apr 2020 02:10:50: 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 02:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.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 02:10:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:10:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:10:55: 10000000 INFO @ Thu, 16 Apr 2020 02:10:57: 5000000 INFO @ Thu, 16 Apr 2020 02:11:01: 1000000 INFO @ Thu, 16 Apr 2020 02:11:02: 11000000 INFO @ Thu, 16 Apr 2020 02:11:03: 6000000 INFO @ Thu, 16 Apr 2020 02:11:07: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:11:07: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:11:07: #1 total tags in treatment: 5615088 INFO @ Thu, 16 Apr 2020 02:11:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:11:07: #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 02:11:07: #1 tags after filtering in treatment: 5462965 INFO @ Thu, 16 Apr 2020 02:11:07: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 02:11:07: #1 finished! INFO @ Thu, 16 Apr 2020 02:11:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:11:07: 2000000 INFO @ Thu, 16 Apr 2020 02:11:08: #2 number of paired peaks: 410 WARNING @ Thu, 16 Apr 2020 02:11:08: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Thu, 16 Apr 2020 02:11:08: start model_add_line... INFO @ Thu, 16 Apr 2020 02:11:08: start X-correlation... INFO @ Thu, 16 Apr 2020 02:11:08: end of X-cor INFO @ Thu, 16 Apr 2020 02:11:08: #2 finished! INFO @ Thu, 16 Apr 2020 02:11:08: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 02:11:08: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 02:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05_model.r INFO @ Thu, 16 Apr 2020 02:11:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:11:10: 7000000 INFO @ Thu, 16 Apr 2020 02:11:14: 3000000 INFO @ Thu, 16 Apr 2020 02:11:16: 8000000 INFO @ Thu, 16 Apr 2020 02:11:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:11:21: 4000000 INFO @ Thu, 16 Apr 2020 02:11:23: 9000000 INFO @ Thu, 16 Apr 2020 02:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.05_summits.bed INFO @ Thu, 16 Apr 2020 02:11:26: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (909 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:11:27: 5000000 INFO @ Thu, 16 Apr 2020 02:11:29: 10000000 INFO @ Thu, 16 Apr 2020 02:11:34: 6000000 INFO @ Thu, 16 Apr 2020 02:11:36: 11000000 INFO @ Thu, 16 Apr 2020 02:11:40: 7000000 INFO @ Thu, 16 Apr 2020 02:11:41: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:11:41: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:11:41: #1 total tags in treatment: 5615088 INFO @ Thu, 16 Apr 2020 02:11:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:11:41: #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 02:11:41: #1 tags after filtering in treatment: 5462965 INFO @ Thu, 16 Apr 2020 02:11:41: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 02:11:41: #1 finished! INFO @ Thu, 16 Apr 2020 02:11:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:11:42: #2 number of paired peaks: 410 WARNING @ Thu, 16 Apr 2020 02:11:42: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Thu, 16 Apr 2020 02:11:42: start model_add_line... INFO @ Thu, 16 Apr 2020 02:11:42: start X-correlation... INFO @ Thu, 16 Apr 2020 02:11:42: end of X-cor INFO @ Thu, 16 Apr 2020 02:11:42: #2 finished! INFO @ Thu, 16 Apr 2020 02:11:42: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 02:11:42: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 02:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10_model.r INFO @ Thu, 16 Apr 2020 02:11:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:11:47: 8000000 INFO @ Thu, 16 Apr 2020 02:11:52: 9000000 INFO @ Thu, 16 Apr 2020 02:11:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:11:58: 10000000 INFO @ Thu, 16 Apr 2020 02:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.10_summits.bed INFO @ Thu, 16 Apr 2020 02:12:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:12:04: 11000000 INFO @ Thu, 16 Apr 2020 02:12:09: #1 tag size is determined as 77 bps INFO @ Thu, 16 Apr 2020 02:12:09: #1 tag size = 77 INFO @ Thu, 16 Apr 2020 02:12:09: #1 total tags in treatment: 5615088 INFO @ Thu, 16 Apr 2020 02:12:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:12:09: #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 02:12:09: #1 tags after filtering in treatment: 5462965 INFO @ Thu, 16 Apr 2020 02:12:09: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 02:12:09: #1 finished! INFO @ Thu, 16 Apr 2020 02:12:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:12:10: #2 number of paired peaks: 410 WARNING @ Thu, 16 Apr 2020 02:12:10: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Thu, 16 Apr 2020 02:12:10: start model_add_line... INFO @ Thu, 16 Apr 2020 02:12:10: start X-correlation... INFO @ Thu, 16 Apr 2020 02:12:10: end of X-cor INFO @ Thu, 16 Apr 2020 02:12:10: #2 finished! INFO @ Thu, 16 Apr 2020 02:12:10: #2 predicted fragment length is 175 bps INFO @ Thu, 16 Apr 2020 02:12:10: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 16 Apr 2020 02:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20_model.r INFO @ Thu, 16 Apr 2020 02:12:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:12:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5309723/SRX5309723.20_summits.bed INFO @ Thu, 16 Apr 2020 02:12:28: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (129 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。