Job ID = 5721024 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:35:42 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 ) 2020-04-15T18:35:42 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 : 20,920,661 reads read : 20,920,661 reads written : 20,920,661 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: 00:05:37 20920661 reads; of these: 20920661 (100.00%) were unpaired; of these: 6962044 (33.28%) aligned 0 times 9845682 (47.06%) aligned exactly 1 time 4112935 (19.66%) aligned >1 times 66.72% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 6598553 / 13958617 = 0.4727 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 03:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.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 03:54:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:54:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:54:51: 1000000 INFO @ Thu, 16 Apr 2020 03:54:56: 2000000 INFO @ Thu, 16 Apr 2020 03:55:01: 3000000 INFO @ Thu, 16 Apr 2020 03:55:06: 4000000 INFO @ Thu, 16 Apr 2020 03:55:11: 5000000 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 03:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.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 03:55:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:55:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:55:17: 6000000 INFO @ Thu, 16 Apr 2020 03:55:22: 7000000 INFO @ Thu, 16 Apr 2020 03:55:23: 1000000 INFO @ Thu, 16 Apr 2020 03:55:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:55:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:55:24: #1 total tags in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:55:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:55:24: #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 03:55:24: #1 tags after filtering in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:55:24: #1 finished! INFO @ Thu, 16 Apr 2020 03:55:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:55:24: #2 number of paired peaks: 203 WARNING @ Thu, 16 Apr 2020 03:55:24: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 16 Apr 2020 03:55:24: start model_add_line... INFO @ Thu, 16 Apr 2020 03:55:24: start X-correlation... INFO @ Thu, 16 Apr 2020 03:55:24: end of X-cor INFO @ Thu, 16 Apr 2020 03:55:24: #2 finished! INFO @ Thu, 16 Apr 2020 03:55:24: #2 predicted fragment length is 65 bps INFO @ Thu, 16 Apr 2020 03:55:24: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 16 Apr 2020 03:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05_model.r WARNING @ Thu, 16 Apr 2020 03:55:24: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:55:24: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 16 Apr 2020 03:55:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:55:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:55:30: 2000000 INFO @ Thu, 16 Apr 2020 03:55:37: 3000000 INFO @ Thu, 16 Apr 2020 03:55:40: #3 Call peaks for each chromosome... 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 03:55:43: 4000000 INFO @ Thu, 16 Apr 2020 03:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.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 03:55:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:55:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.05_summits.bed INFO @ Thu, 16 Apr 2020 03:55:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:55:51: 5000000 INFO @ Thu, 16 Apr 2020 03:55:52: 1000000 INFO @ Thu, 16 Apr 2020 03:55:58: 6000000 INFO @ Thu, 16 Apr 2020 03:55:58: 2000000 INFO @ Thu, 16 Apr 2020 03:56:05: 3000000 INFO @ Thu, 16 Apr 2020 03:56:05: 7000000 INFO @ Thu, 16 Apr 2020 03:56:07: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:56:07: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:56:07: #1 total tags in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:56:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:56:07: #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 03:56:07: #1 tags after filtering in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:56:07: #1 finished! INFO @ Thu, 16 Apr 2020 03:56:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:56:08: #2 number of paired peaks: 203 WARNING @ Thu, 16 Apr 2020 03:56:08: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 16 Apr 2020 03:56:08: start model_add_line... INFO @ Thu, 16 Apr 2020 03:56:08: start X-correlation... INFO @ Thu, 16 Apr 2020 03:56:08: end of X-cor INFO @ Thu, 16 Apr 2020 03:56:08: #2 finished! INFO @ Thu, 16 Apr 2020 03:56:08: #2 predicted fragment length is 65 bps INFO @ Thu, 16 Apr 2020 03:56:08: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 16 Apr 2020 03:56:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10_model.r WARNING @ Thu, 16 Apr 2020 03:56:08: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:56:08: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 16 Apr 2020 03:56:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:56:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:56:11: 4000000 INFO @ Thu, 16 Apr 2020 03:56:17: 5000000 INFO @ Thu, 16 Apr 2020 03:56:23: 6000000 INFO @ Thu, 16 Apr 2020 03:56:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:56:29: 7000000 INFO @ Thu, 16 Apr 2020 03:56:31: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:56:31: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:56:31: #1 total tags in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:56:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:56:31: #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 03:56:31: #1 tags after filtering in treatment: 7360064 INFO @ Thu, 16 Apr 2020 03:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:56:31: #1 finished! INFO @ Thu, 16 Apr 2020 03:56:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:56:31: #2 number of paired peaks: 203 WARNING @ Thu, 16 Apr 2020 03:56:31: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 16 Apr 2020 03:56:31: start model_add_line... INFO @ Thu, 16 Apr 2020 03:56:31: start X-correlation... INFO @ Thu, 16 Apr 2020 03:56:31: end of X-cor INFO @ Thu, 16 Apr 2020 03:56:31: #2 finished! INFO @ Thu, 16 Apr 2020 03:56:31: #2 predicted fragment length is 65 bps INFO @ Thu, 16 Apr 2020 03:56:31: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 16 Apr 2020 03:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20_model.r WARNING @ Thu, 16 Apr 2020 03:56:31: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:56:31: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 16 Apr 2020 03:56:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:56:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:56:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.10_summits.bed INFO @ Thu, 16 Apr 2020 03:56:32: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (490 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:56:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386767/SRX6386767.20_summits.bed INFO @ Thu, 16 Apr 2020 03:56:53: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (200 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。