Job ID = 14171356 SRX = SRX8512931 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6901609 spots for SRR11969177/SRR11969177.sra Written 6901609 spots for SRR11969177/SRR11969177.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171823 ("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: 00:04:26 6901609 reads; of these: 6901609 (100.00%) were unpaired; of these: 885 (0.01%) aligned 0 times 5990315 (86.80%) aligned exactly 1 time 910409 (13.19%) aligned >1 times 99.99% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 481287 / 6900724 = 0.0697 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 11:31:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.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 11:31:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:31:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:00: 1000000 INFO @ Sat, 11 Dec 2021 11:32:08: 2000000 INFO @ Sat, 11 Dec 2021 11:32:17: 3000000 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 11:32:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.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 11:32:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:27: 4000000 INFO @ Sat, 11 Dec 2021 11:32:31: 1000000 INFO @ Sat, 11 Dec 2021 11:32:37: 5000000 INFO @ Sat, 11 Dec 2021 11:32:41: 2000000 INFO @ Sat, 11 Dec 2021 11:32:47: 6000000 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 11:32:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.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 11:32:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:32:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:32:51: 3000000 INFO @ Sat, 11 Dec 2021 11:32:51: #1 tag size is determined as 131 bps INFO @ Sat, 11 Dec 2021 11:32:51: #1 tag size = 131 INFO @ Sat, 11 Dec 2021 11:32:51: #1 total tags in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:32:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:32:51: #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 11:32:51: #1 tags after filtering in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:32:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:32:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:32:52: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 11:32:52: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 11:32:52: start model_add_line... INFO @ Sat, 11 Dec 2021 11:32:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:32:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:32:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:32:52: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 11:32:52: #2 alternative fragment length(s) may be 4,138,546 bps INFO @ Sat, 11 Dec 2021 11:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05_model.r WARNING @ Sat, 11 Dec 2021 11:32:52: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:32:52: #2 You may need to consider one of the other alternative d(s): 4,138,546 WARNING @ Sat, 11 Dec 2021 11:32:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:32:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:33:01: 1000000 INFO @ Sat, 11 Dec 2021 11:33:01: 4000000 INFO @ Sat, 11 Dec 2021 11:33:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:11: 2000000 INFO @ Sat, 11 Dec 2021 11:33:12: 5000000 INFO @ Sat, 11 Dec 2021 11:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.05_summits.bed INFO @ Sat, 11 Dec 2021 11:33:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:33:21: 3000000 INFO @ Sat, 11 Dec 2021 11:33:22: 6000000 INFO @ Sat, 11 Dec 2021 11:33:26: #1 tag size is determined as 131 bps INFO @ Sat, 11 Dec 2021 11:33:26: #1 tag size = 131 INFO @ Sat, 11 Dec 2021 11:33:26: #1 total tags in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:33:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:33:26: #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 11:33:26: #1 tags after filtering in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:33:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:33:26: #1 finished! INFO @ Sat, 11 Dec 2021 11:33:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:33:27: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 11:33:27: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 11:33:27: start model_add_line... INFO @ Sat, 11 Dec 2021 11:33:27: start X-correlation... INFO @ Sat, 11 Dec 2021 11:33:27: end of X-cor INFO @ Sat, 11 Dec 2021 11:33:27: #2 finished! INFO @ Sat, 11 Dec 2021 11:33:27: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 11:33:27: #2 alternative fragment length(s) may be 4,138,546 bps INFO @ Sat, 11 Dec 2021 11:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10_model.r WARNING @ Sat, 11 Dec 2021 11:33:27: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:33:27: #2 You may need to consider one of the other alternative d(s): 4,138,546 WARNING @ Sat, 11 Dec 2021 11:33:27: #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 11:33:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:33:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:33:40: 5000000 INFO @ Sat, 11 Dec 2021 11:33:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.10_summits.bed INFO @ Sat, 11 Dec 2021 11:33:47: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:33:48: 6000000 INFO @ Sat, 11 Dec 2021 11:33:52: #1 tag size is determined as 131 bps INFO @ Sat, 11 Dec 2021 11:33:52: #1 tag size = 131 INFO @ Sat, 11 Dec 2021 11:33:52: #1 total tags in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:33:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:33:52: #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 11:33:52: #1 tags after filtering in treatment: 6419437 INFO @ Sat, 11 Dec 2021 11:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:33:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:33:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:33:52: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 11:33:52: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 11:33:52: start model_add_line... INFO @ Sat, 11 Dec 2021 11:33:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:33:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:33:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:33:52: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 11:33:52: #2 alternative fragment length(s) may be 4,138,546 bps INFO @ Sat, 11 Dec 2021 11:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20_model.r WARNING @ Sat, 11 Dec 2021 11:33:52: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:33:52: #2 You may need to consider one of the other alternative d(s): 4,138,546 WARNING @ Sat, 11 Dec 2021 11:33:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:33:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:34:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512931/SRX8512931.20_summits.bed INFO @ Sat, 11 Dec 2021 11:34:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling