Job ID = 14170493 SRX = SRX8689054 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5174911 spots for SRR12174368/SRR12174368.sra Written 5174911 spots for SRR12174368/SRR12174368.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170891 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:31 5174911 reads; of these: 5174911 (100.00%) were unpaired; of these: 124407 (2.40%) aligned 0 times 3914639 (75.65%) aligned exactly 1 time 1135865 (21.95%) aligned >1 times 97.60% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 191278 / 5050504 = 0.0379 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.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 @ Sat, 11 Dec 2021 07:00:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:18: 1000000 INFO @ Sat, 11 Dec 2021 07:00:23: 2000000 INFO @ Sat, 11 Dec 2021 07:00:29: 3000000 INFO @ Sat, 11 Dec 2021 07:00:34: 4000000 INFO @ Sat, 11 Dec 2021 07:00:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:39: #1 total tags in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:00:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:00:39: #1 tags after filtering in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:39: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:39: #2 number of paired peaks: 255 WARNING @ Sat, 11 Dec 2021 07:00:39: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:39: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:39: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:39: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:39: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:39: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:00:39: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05_model.r WARNING @ Sat, 11 Dec 2021 07:00:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:00:39: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:00:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:00:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:39: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.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 @ Sat, 11 Dec 2021 07:00:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:47: 1000000 INFO @ Sat, 11 Dec 2021 07:00:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:00:53: 2000000 INFO @ Sat, 11 Dec 2021 07:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.05_summits.bed INFO @ Sat, 11 Dec 2021 07:00:55: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1012 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:00:59: 3000000 INFO @ Sat, 11 Dec 2021 07:01:04: 4000000 INFO @ Sat, 11 Dec 2021 07:01:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:09: #1 total tags in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:01:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:01:09: #1 tags after filtering in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:09: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:09: #2 number of paired peaks: 255 WARNING @ Sat, 11 Dec 2021 07:01:09: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:09: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:09: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:09: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:09: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:09: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:01:09: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10_model.r WARNING @ Sat, 11 Dec 2021 07:01:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:09: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:01:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:01:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.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 @ Sat, 11 Dec 2021 07:01:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:17: 1000000 INFO @ Sat, 11 Dec 2021 07:01:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:23: 2000000 INFO @ Sat, 11 Dec 2021 07:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.10_summits.bed INFO @ Sat, 11 Dec 2021 07:01:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:28: 3000000 INFO @ Sat, 11 Dec 2021 07:01:34: 4000000 INFO @ Sat, 11 Dec 2021 07:01:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:39: #1 total tags in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:01:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:01:39: #1 tags after filtering in treatment: 4859226 INFO @ Sat, 11 Dec 2021 07:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:39: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:39: #2 number of paired peaks: 255 WARNING @ Sat, 11 Dec 2021 07:01:39: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:39: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:39: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:39: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:39: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:39: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:01:39: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20_model.r WARNING @ Sat, 11 Dec 2021 07:01:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:39: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:01:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:01:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:01:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689054/SRX8689054.20_summits.bed INFO @ Sat, 11 Dec 2021 07:01:54: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (466 records, 4 fields): 2 millis CompletedMACS2peakCalling