Job ID = 5720941 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:24:53 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 ) 2020-04-15T18:24:53 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 ) 2020-04-15T18:24:53 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 : 8,520,207 reads read : 8,520,207 reads written : 8,520,207 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: 00:02:53 8520207 reads; of these: 8520207 (100.00%) were unpaired; of these: 453326 (5.32%) aligned 0 times 5486084 (64.39%) aligned exactly 1 time 2580797 (30.29%) aligned >1 times 94.68% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 927290 / 8066881 = 0.1150 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 03:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.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 03:30:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:30:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:30:45: 1000000 INFO @ Thu, 16 Apr 2020 03:30:51: 2000000 INFO @ Thu, 16 Apr 2020 03:30:57: 3000000 INFO @ Thu, 16 Apr 2020 03:31:02: 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 03:31:08: 5000000 INFO @ Thu, 16 Apr 2020 03:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.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 03:31:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:31:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:31:13: 6000000 INFO @ Thu, 16 Apr 2020 03:31:15: 1000000 INFO @ Thu, 16 Apr 2020 03:31:19: 7000000 INFO @ Thu, 16 Apr 2020 03:31:20: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:31:20: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:31:20: #1 total tags in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:31:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:31:20: #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 03:31:20: #1 tags after filtering in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:31:20: #1 finished! INFO @ Thu, 16 Apr 2020 03:31:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:31:21: #2 number of paired peaks: 233 WARNING @ Thu, 16 Apr 2020 03:31:21: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Thu, 16 Apr 2020 03:31:21: start model_add_line... INFO @ Thu, 16 Apr 2020 03:31:21: start X-correlation... INFO @ Thu, 16 Apr 2020 03:31:21: end of X-cor INFO @ Thu, 16 Apr 2020 03:31:21: #2 finished! INFO @ Thu, 16 Apr 2020 03:31:21: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 03:31:21: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 03:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05_model.r WARNING @ Thu, 16 Apr 2020 03:31:21: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:31:21: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 03:31:21: #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 03:31:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:31:21: 2000000 INFO @ Thu, 16 Apr 2020 03:31:27: 3000000 INFO @ Thu, 16 Apr 2020 03:31:33: 4000000 INFO @ Thu, 16 Apr 2020 03:31:35: #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 03:31:38: 5000000 INFO @ Thu, 16 Apr 2020 03:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.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 03:31:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:31:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.05_summits.bed INFO @ Thu, 16 Apr 2020 03:31:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1277 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:31:44: 6000000 INFO @ Thu, 16 Apr 2020 03:31:46: 1000000 INFO @ Thu, 16 Apr 2020 03:31:50: 7000000 INFO @ Thu, 16 Apr 2020 03:31:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:31:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:31:51: #1 total tags in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:31:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:31:51: #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 03:31:51: #1 tags after filtering in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:31:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:31:51: #1 finished! INFO @ Thu, 16 Apr 2020 03:31:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:31:52: #2 number of paired peaks: 233 WARNING @ Thu, 16 Apr 2020 03:31:52: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Thu, 16 Apr 2020 03:31:52: start model_add_line... INFO @ Thu, 16 Apr 2020 03:31:52: start X-correlation... INFO @ Thu, 16 Apr 2020 03:31:52: end of X-cor INFO @ Thu, 16 Apr 2020 03:31:52: #2 finished! INFO @ Thu, 16 Apr 2020 03:31:52: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 03:31:52: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 03:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10_model.r WARNING @ Thu, 16 Apr 2020 03:31:52: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:31:52: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 03:31:52: #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 03:31:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:31:52: 2000000 INFO @ Thu, 16 Apr 2020 03:31:59: 3000000 INFO @ Thu, 16 Apr 2020 03:32:05: 4000000 INFO @ Thu, 16 Apr 2020 03:32:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:32:11: 5000000 INFO @ Thu, 16 Apr 2020 03:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.10_summits.bed INFO @ Thu, 16 Apr 2020 03:32:14: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (944 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:32:17: 6000000 INFO @ Thu, 16 Apr 2020 03:32:23: 7000000 INFO @ Thu, 16 Apr 2020 03:32:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:32:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:32:24: #1 total tags in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:32:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:32:24: #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 03:32:24: #1 tags after filtering in treatment: 7139591 INFO @ Thu, 16 Apr 2020 03:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:32:24: #1 finished! INFO @ Thu, 16 Apr 2020 03:32:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:32:25: #2 number of paired peaks: 233 WARNING @ Thu, 16 Apr 2020 03:32:25: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Thu, 16 Apr 2020 03:32:25: start model_add_line... INFO @ Thu, 16 Apr 2020 03:32:25: start X-correlation... INFO @ Thu, 16 Apr 2020 03:32:25: end of X-cor INFO @ Thu, 16 Apr 2020 03:32:25: #2 finished! INFO @ Thu, 16 Apr 2020 03:32:25: #2 predicted fragment length is 54 bps INFO @ Thu, 16 Apr 2020 03:32:25: #2 alternative fragment length(s) may be 54 bps INFO @ Thu, 16 Apr 2020 03:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20_model.r WARNING @ Thu, 16 Apr 2020 03:32:25: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:32:25: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Thu, 16 Apr 2020 03:32:25: #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 03:32:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:32:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386740/SRX6386740.20_summits.bed INFO @ Thu, 16 Apr 2020 03:32:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (564 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。