Job ID = 12264892 SRX = SRX3032290 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9425766 spots for SRR5863980/SRR5863980.sra Written 9425766 spots for SRR5863980/SRR5863980.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265064 ("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: 00:04:57 9425766 reads; of these: 9425766 (100.00%) were unpaired; of these: 2125014 (22.54%) aligned 0 times 5616298 (59.58%) aligned exactly 1 time 1684454 (17.87%) aligned >1 times 77.46% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 1187962 / 7300752 = 0.1627 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.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, 03 Apr 2021 06:03:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:39: 1000000 INFO @ Sat, 03 Apr 2021 06:03:48: 2000000 INFO @ Sat, 03 Apr 2021 06:03:56: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.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, 03 Apr 2021 06:04:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:04: 4000000 INFO @ Sat, 03 Apr 2021 06:04:09: 1000000 INFO @ Sat, 03 Apr 2021 06:04:12: 5000000 INFO @ Sat, 03 Apr 2021 06:04:18: 2000000 INFO @ Sat, 03 Apr 2021 06:04:20: 6000000 INFO @ Sat, 03 Apr 2021 06:04:21: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:04:21: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:04:21: #1 total tags in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:04:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:04:22: #1 tags after filtering in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:22: #2 number of paired peaks: 438 WARNING @ Sat, 03 Apr 2021 06:04:22: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Apr 2021 06:04:22: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:22: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:22: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:22: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:22: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 06:04:22: #2 alternative fragment length(s) may be 73,91,583 bps INFO @ Sat, 03 Apr 2021 06:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05_model.r WARNING @ Sat, 03 Apr 2021 06:04:22: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:22: #2 You may need to consider one of the other alternative d(s): 73,91,583 WARNING @ Sat, 03 Apr 2021 06:04:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:04:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:26: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.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, 03 Apr 2021 06:04:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:34: 4000000 INFO @ Sat, 03 Apr 2021 06:04:39: 1000000 INFO @ Sat, 03 Apr 2021 06:04:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:42: 5000000 INFO @ Sat, 03 Apr 2021 06:04:46: 2000000 INFO @ Sat, 03 Apr 2021 06:04:50: 6000000 INFO @ Sat, 03 Apr 2021 06:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.05_summits.bed INFO @ Sat, 03 Apr 2021 06:04:51: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2817 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:04:51: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:04:51: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:04:51: #1 total tags in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:04:51: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:04:52: #1 tags after filtering in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:52: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:52: #2 number of paired peaks: 438 WARNING @ Sat, 03 Apr 2021 06:04:52: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Apr 2021 06:04:52: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:52: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:52: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:52: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:52: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 06:04:52: #2 alternative fragment length(s) may be 73,91,583 bps INFO @ Sat, 03 Apr 2021 06:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10_model.r WARNING @ Sat, 03 Apr 2021 06:04:52: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:52: #2 You may need to consider one of the other alternative d(s): 73,91,583 WARNING @ Sat, 03 Apr 2021 06:04:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:04:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:54: 3000000 INFO @ Sat, 03 Apr 2021 06:05:02: 4000000 INFO @ Sat, 03 Apr 2021 06:05:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:05:19: 6000000 INFO @ Sat, 03 Apr 2021 06:05:20: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:05:20: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:05:20: #1 total tags in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:05:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:05:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:05:20: #1 tags after filtering in treatment: 6112790 INFO @ Sat, 03 Apr 2021 06:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:05:20: #1 finished! INFO @ Sat, 03 Apr 2021 06:05:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.10_summits.bed INFO @ Sat, 03 Apr 2021 06:05:20: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:05:21: #2 number of paired peaks: 438 WARNING @ Sat, 03 Apr 2021 06:05:21: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Apr 2021 06:05:21: start model_add_line... INFO @ Sat, 03 Apr 2021 06:05:21: start X-correlation... INFO @ Sat, 03 Apr 2021 06:05:21: end of X-cor INFO @ Sat, 03 Apr 2021 06:05:21: #2 finished! INFO @ Sat, 03 Apr 2021 06:05:21: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Apr 2021 06:05:21: #2 alternative fragment length(s) may be 73,91,583 bps INFO @ Sat, 03 Apr 2021 06:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20_model.r WARNING @ Sat, 03 Apr 2021 06:05:21: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:05:21: #2 You may need to consider one of the other alternative d(s): 73,91,583 WARNING @ Sat, 03 Apr 2021 06:05:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:05:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:05:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:05:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032290/SRX3032290.20_summits.bed INFO @ Sat, 03 Apr 2021 06:05:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling