Job ID = 5720878 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:43:33 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 ) 2020-04-15T17:43:33 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 : 20,215,194 reads read : 20,215,194 reads written : 20,215,194 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:01 20215194 reads; of these: 20215194 (100.00%) were unpaired; of these: 10642513 (52.65%) aligned 0 times 6502690 (32.17%) aligned exactly 1 time 3069991 (15.19%) aligned >1 times 47.35% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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_rmdupse_core] 5511508 / 9572681 = 0.5758 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 03:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.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 03:01:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:01:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:01:27: 1000000 INFO @ Thu, 16 Apr 2020 03:01:33: 2000000 INFO @ Thu, 16 Apr 2020 03:01:39: 3000000 INFO @ Thu, 16 Apr 2020 03:01:45: 4000000 INFO @ Thu, 16 Apr 2020 03:01:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:01:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:01:45: #1 total tags in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:01:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:01:45: #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 03:01:45: #1 tags after filtering in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:01:45: #1 finished! INFO @ Thu, 16 Apr 2020 03:01:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:01:45: #2 number of paired peaks: 900 WARNING @ Thu, 16 Apr 2020 03:01:45: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Thu, 16 Apr 2020 03:01:45: start model_add_line... INFO @ Thu, 16 Apr 2020 03:01:45: start X-correlation... INFO @ Thu, 16 Apr 2020 03:01:45: end of X-cor INFO @ Thu, 16 Apr 2020 03:01:45: #2 finished! INFO @ Thu, 16 Apr 2020 03:01:45: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:01:45: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05_model.r WARNING @ Thu, 16 Apr 2020 03:01:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:01:45: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:01:45: #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 03:01:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:01:45: #3 Pre-compute pvalue-qvalue table... 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 03:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.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 03:01:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:01:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:01:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:01:57: 1000000 INFO @ Thu, 16 Apr 2020 03:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.05_summits.bed INFO @ Thu, 16 Apr 2020 03:02:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2421 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:02:03: 2000000 INFO @ Thu, 16 Apr 2020 03:02:09: 3000000 INFO @ Thu, 16 Apr 2020 03:02:15: 4000000 INFO @ Thu, 16 Apr 2020 03:02:15: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:02:15: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:02:15: #1 total tags in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:02:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:02:15: #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 03:02:15: #1 tags after filtering in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:02:15: #1 finished! INFO @ Thu, 16 Apr 2020 03:02:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:02:15: #2 number of paired peaks: 900 WARNING @ Thu, 16 Apr 2020 03:02:15: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Thu, 16 Apr 2020 03:02:15: start model_add_line... INFO @ Thu, 16 Apr 2020 03:02:15: start X-correlation... INFO @ Thu, 16 Apr 2020 03:02:15: end of X-cor INFO @ Thu, 16 Apr 2020 03:02:15: #2 finished! INFO @ Thu, 16 Apr 2020 03:02:15: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:02:15: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10_model.r WARNING @ Thu, 16 Apr 2020 03:02:15: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:02:15: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:02:15: #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 03:02:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:02:15: #3 Pre-compute pvalue-qvalue table... 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 03:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.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 03:02:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:02:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:02:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:02:27: 1000000 INFO @ Thu, 16 Apr 2020 03:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.10_summits.bed INFO @ Thu, 16 Apr 2020 03:02:29: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1198 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:02:33: 2000000 INFO @ Thu, 16 Apr 2020 03:02:39: 3000000 INFO @ Thu, 16 Apr 2020 03:02:45: 4000000 INFO @ Thu, 16 Apr 2020 03:02:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:02:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:02:45: #1 total tags in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:02:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:02:45: #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 03:02:45: #1 tags after filtering in treatment: 4061173 INFO @ Thu, 16 Apr 2020 03:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:02:45: #1 finished! INFO @ Thu, 16 Apr 2020 03:02:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:02:46: #2 number of paired peaks: 900 WARNING @ Thu, 16 Apr 2020 03:02:46: Fewer paired peaks (900) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 900 pairs to build model! INFO @ Thu, 16 Apr 2020 03:02:46: start model_add_line... INFO @ Thu, 16 Apr 2020 03:02:46: start X-correlation... INFO @ Thu, 16 Apr 2020 03:02:46: end of X-cor INFO @ Thu, 16 Apr 2020 03:02:46: #2 finished! INFO @ Thu, 16 Apr 2020 03:02:46: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:02:46: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20_model.r WARNING @ Thu, 16 Apr 2020 03:02:46: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:02:46: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:02:46: #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 03:02:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:02:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:02:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:02:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:02:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775906/SRX5775906.20_summits.bed INFO @ Thu, 16 Apr 2020 03:02:59: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (626 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。