Job ID = 14171333 SRX = SRX9986152 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14983892 spots for SRR13591563/SRR13591563.sra Written 14983892 spots for SRR13591563/SRR13591563.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171806 ("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: 00:04:48 14983892 reads; of these: 14983892 (100.00%) were unpaired; of these: 2666907 (17.80%) aligned 0 times 9260926 (61.81%) aligned exactly 1 time 3056059 (20.40%) aligned >1 times 82.20% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 1901251 / 12316985 = 0.1544 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 11:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.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 11:28:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:28:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:28:10: 1000000 INFO @ Sat, 11 Dec 2021 11:28:18: 2000000 INFO @ Sat, 11 Dec 2021 11:28:25: 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 11:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.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 11:28:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:28:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:28:33: 4000000 INFO @ Sat, 11 Dec 2021 11:28:40: 1000000 INFO @ Sat, 11 Dec 2021 11:28:41: 5000000 INFO @ Sat, 11 Dec 2021 11:28:47: 2000000 INFO @ Sat, 11 Dec 2021 11:28:48: 6000000 INFO @ Sat, 11 Dec 2021 11:28:54: 3000000 INFO @ Sat, 11 Dec 2021 11:28:56: 7000000 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 11:29:02: 4000000 INFO @ Sat, 11 Dec 2021 11:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.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 11:29:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:29:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:29:03: 8000000 INFO @ Sat, 11 Dec 2021 11:29:10: 1000000 INFO @ Sat, 11 Dec 2021 11:29:10: 5000000 INFO @ Sat, 11 Dec 2021 11:29:11: 9000000 INFO @ Sat, 11 Dec 2021 11:29:17: 6000000 INFO @ Sat, 11 Dec 2021 11:29:17: 2000000 INFO @ Sat, 11 Dec 2021 11:29:18: 10000000 INFO @ Sat, 11 Dec 2021 11:29:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:29:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:29:22: #1 total tags in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:29:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:29:22: #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 11:29:22: #1 tags after filtering in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:29:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:29:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:29:23: #2 number of paired peaks: 132 WARNING @ Sat, 11 Dec 2021 11:29:23: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 11 Dec 2021 11:29:23: start model_add_line... INFO @ Sat, 11 Dec 2021 11:29:23: start X-correlation... INFO @ Sat, 11 Dec 2021 11:29:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:29:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:29:23: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 11:29:23: #2 alternative fragment length(s) may be 44,98,127,246,289,304,425,465,480,514,534,551,574,593 bps INFO @ Sat, 11 Dec 2021 11:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05_model.r WARNING @ Sat, 11 Dec 2021 11:29:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:29:23: #2 You may need to consider one of the other alternative d(s): 44,98,127,246,289,304,425,465,480,514,534,551,574,593 WARNING @ Sat, 11 Dec 2021 11:29:23: #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 11:29:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:29:25: 7000000 INFO @ Sat, 11 Dec 2021 11:29:25: 3000000 INFO @ Sat, 11 Dec 2021 11:29:32: 8000000 INFO @ Sat, 11 Dec 2021 11:29:32: 4000000 INFO @ Sat, 11 Dec 2021 11:29:40: 9000000 INFO @ Sat, 11 Dec 2021 11:29:41: 5000000 INFO @ Sat, 11 Dec 2021 11:29:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:29:47: 10000000 INFO @ Sat, 11 Dec 2021 11:29:48: 6000000 INFO @ Sat, 11 Dec 2021 11:29:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:29:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:29:51: #1 total tags in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:29:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:29:51: #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 11:29:51: #1 tags after filtering in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:29:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:29:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:29:51: #2 number of paired peaks: 132 WARNING @ Sat, 11 Dec 2021 11:29:51: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 11 Dec 2021 11:29:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:29:52: start X-correlation... INFO @ Sat, 11 Dec 2021 11:29:52: end of X-cor INFO @ Sat, 11 Dec 2021 11:29:52: #2 finished! INFO @ Sat, 11 Dec 2021 11:29:52: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 11:29:52: #2 alternative fragment length(s) may be 44,98,127,246,289,304,425,465,480,514,534,551,574,593 bps INFO @ Sat, 11 Dec 2021 11:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10_model.r WARNING @ Sat, 11 Dec 2021 11:29:52: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:29:52: #2 You may need to consider one of the other alternative d(s): 44,98,127,246,289,304,425,465,480,514,534,551,574,593 WARNING @ Sat, 11 Dec 2021 11:29:52: #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 11:29:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.05_summits.bed INFO @ Sat, 11 Dec 2021 11:29:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:29:56: 7000000 INFO @ Sat, 11 Dec 2021 11:30:03: 8000000 INFO @ Sat, 11 Dec 2021 11:30:11: 9000000 INFO @ Sat, 11 Dec 2021 11:30:11: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:30:19: 10000000 INFO @ Sat, 11 Dec 2021 11:30:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:30:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:30:21: #1 total tags in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:30:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:30:21: #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 11:30:22: #1 tags after filtering in treatment: 10415734 INFO @ Sat, 11 Dec 2021 11:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:30:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:30:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:30:22: #2 number of paired peaks: 132 WARNING @ Sat, 11 Dec 2021 11:30:22: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 11 Dec 2021 11:30:22: start model_add_line... INFO @ Sat, 11 Dec 2021 11:30:22: start X-correlation... INFO @ Sat, 11 Dec 2021 11:30:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:30:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:30:23: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 11:30:23: #2 alternative fragment length(s) may be 44,98,127,246,289,304,425,465,480,514,534,551,574,593 bps INFO @ Sat, 11 Dec 2021 11:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20_model.r WARNING @ Sat, 11 Dec 2021 11:30:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:30:23: #2 You may need to consider one of the other alternative d(s): 44,98,127,246,289,304,425,465,480,514,534,551,574,593 WARNING @ Sat, 11 Dec 2021 11:30:23: #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 11:30:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:30:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.10_summits.bed INFO @ Sat, 11 Dec 2021 11:30:23: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:30:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986152/SRX9986152.20_summits.bed INFO @ Sat, 11 Dec 2021 11:30:54: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (48 records, 4 fields): 12 millis CompletedMACS2peakCalling