Job ID = 14167242 SRX = SRX8688907 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7775380 spots for SRR12174259/SRR12174259.sra Written 7775380 spots for SRR12174259/SRR12174259.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167807 ("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: 00:03:02 7775380 reads; of these: 7775380 (100.00%) were unpaired; of these: 550476 (7.08%) aligned 0 times 4489205 (57.74%) aligned exactly 1 time 2735699 (35.18%) aligned >1 times 92.92% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 571405 / 7224904 = 0.0791 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 @ Fri, 10 Dec 2021 11:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.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 @ Fri, 10 Dec 2021 11:19:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:19:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:19:20: 1000000 INFO @ Fri, 10 Dec 2021 11:19:27: 2000000 INFO @ Fri, 10 Dec 2021 11:19:33: 3000000 INFO @ Fri, 10 Dec 2021 11:19:40: 4000000 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 @ Fri, 10 Dec 2021 11:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.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 @ Fri, 10 Dec 2021 11:19:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:19:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:19:47: 5000000 INFO @ Fri, 10 Dec 2021 11:19:49: 1000000 INFO @ Fri, 10 Dec 2021 11:19:54: 6000000 INFO @ Fri, 10 Dec 2021 11:19:56: 2000000 INFO @ Fri, 10 Dec 2021 11:19:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:19:59: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:19:59: #1 total tags in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:19:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:19:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:19:59: #1 tags after filtering in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:19:59: #1 finished! INFO @ Fri, 10 Dec 2021 11:19:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:19:59: #2 number of paired peaks: 534 WARNING @ Fri, 10 Dec 2021 11:19:59: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 10 Dec 2021 11:19:59: start model_add_line... INFO @ Fri, 10 Dec 2021 11:19:59: start X-correlation... INFO @ Fri, 10 Dec 2021 11:19:59: end of X-cor INFO @ Fri, 10 Dec 2021 11:19:59: #2 finished! INFO @ Fri, 10 Dec 2021 11:19:59: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:19:59: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05_model.r WARNING @ Fri, 10 Dec 2021 11:19:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:19:59: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:19:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:19:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:19:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:20:02: 3000000 INFO @ Fri, 10 Dec 2021 11:20:07: 4000000 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 @ Fri, 10 Dec 2021 11:20:12: 5000000 INFO @ Fri, 10 Dec 2021 11:20:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.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 @ Fri, 10 Dec 2021 11:20:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:19: 6000000 INFO @ Fri, 10 Dec 2021 11:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.05_summits.bed INFO @ Fri, 10 Dec 2021 11:20:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:20:20: 1000000 INFO @ Fri, 10 Dec 2021 11:20:23: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:20:23: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:20:23: #1 total tags in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:20:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:20:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:20:23: #1 tags after filtering in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:20:23: #1 finished! INFO @ Fri, 10 Dec 2021 11:20:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:20:23: #2 number of paired peaks: 534 WARNING @ Fri, 10 Dec 2021 11:20:23: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 10 Dec 2021 11:20:23: start model_add_line... INFO @ Fri, 10 Dec 2021 11:20:23: start X-correlation... INFO @ Fri, 10 Dec 2021 11:20:23: end of X-cor INFO @ Fri, 10 Dec 2021 11:20:23: #2 finished! INFO @ Fri, 10 Dec 2021 11:20:23: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:20:23: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10_model.r WARNING @ Fri, 10 Dec 2021 11:20:23: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:20:23: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:20:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:20:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:20:27: 2000000 INFO @ Fri, 10 Dec 2021 11:20:33: 3000000 INFO @ Fri, 10 Dec 2021 11:20:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:20:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.10_summits.bed INFO @ Fri, 10 Dec 2021 11:20:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:20:47: 5000000 INFO @ Fri, 10 Dec 2021 11:20:53: 6000000 INFO @ Fri, 10 Dec 2021 11:20:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:20:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:20:57: #1 total tags in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:20:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:20:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:20:58: #1 tags after filtering in treatment: 6653499 INFO @ Fri, 10 Dec 2021 11:20:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:20:58: #1 finished! INFO @ Fri, 10 Dec 2021 11:20:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:20:58: #2 number of paired peaks: 534 WARNING @ Fri, 10 Dec 2021 11:20:58: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 10 Dec 2021 11:20:58: start model_add_line... INFO @ Fri, 10 Dec 2021 11:20:58: start X-correlation... INFO @ Fri, 10 Dec 2021 11:20:58: end of X-cor INFO @ Fri, 10 Dec 2021 11:20:58: #2 finished! INFO @ Fri, 10 Dec 2021 11:20:58: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:20:58: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20_model.r WARNING @ Fri, 10 Dec 2021 11:20:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:20:58: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:20:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:20:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:20:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:21:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:21:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:21:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:21:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688907/SRX8688907.20_summits.bed INFO @ Fri, 10 Dec 2021 11:21:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1000 records, 4 fields): 3 millis CompletedMACS2peakCalling