Job ID = 14170546 SRX = SRX8689089 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7501561 spots for SRR12174281/SRR12174281.sra Written 7501561 spots for SRR12174281/SRR12174281.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170943 ("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: 00:02:34 7501561 reads; of these: 7501561 (100.00%) were unpaired; of these: 315229 (4.20%) aligned 0 times 4751011 (63.33%) aligned exactly 1 time 2435321 (32.46%) aligned >1 times 95.80% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 372457 / 7186332 = 0.0518 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 07:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.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 07:14:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:14:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:14:49: 1000000 INFO @ Sat, 11 Dec 2021 07:14:54: 2000000 INFO @ Sat, 11 Dec 2021 07:15:00: 3000000 INFO @ Sat, 11 Dec 2021 07:15:06: 4000000 INFO @ Sat, 11 Dec 2021 07:15:11: 5000000 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 07:15:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.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 07:15:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:15:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:15:17: 6000000 INFO @ Sat, 11 Dec 2021 07:15:19: 1000000 INFO @ Sat, 11 Dec 2021 07:15:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:15:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:15:22: #1 total tags in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:15:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:15:22: #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 07:15:22: #1 tags after filtering in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:15:22: #1 finished! INFO @ Sat, 11 Dec 2021 07:15:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:15:23: #2 number of paired peaks: 349 WARNING @ Sat, 11 Dec 2021 07:15:23: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 11 Dec 2021 07:15:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:15:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:15:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:15:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:15:23: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:15:23: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05_model.r WARNING @ Sat, 11 Dec 2021 07:15:23: #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 07:15:23: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:15:23: #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 07:15:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:15:24: 2000000 INFO @ Sat, 11 Dec 2021 07:15:29: 3000000 INFO @ Sat, 11 Dec 2021 07:15:34: 4000000 INFO @ Sat, 11 Dec 2021 07:15:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:15:39: 5000000 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 07:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.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 07:15:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:15:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.05_summits.bed INFO @ Sat, 11 Dec 2021 07:15:44: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1466 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:15:44: 6000000 INFO @ Sat, 11 Dec 2021 07:15:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:15:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:15:48: #1 total tags in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:15:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:15:48: #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 07:15:49: #1 tags after filtering in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:15:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:15:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:15:49: 1000000 INFO @ Sat, 11 Dec 2021 07:15:49: #2 number of paired peaks: 349 WARNING @ Sat, 11 Dec 2021 07:15:49: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 11 Dec 2021 07:15:49: start model_add_line... INFO @ Sat, 11 Dec 2021 07:15:49: start X-correlation... INFO @ Sat, 11 Dec 2021 07:15:49: end of X-cor INFO @ Sat, 11 Dec 2021 07:15:49: #2 finished! INFO @ Sat, 11 Dec 2021 07:15:49: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:15:49: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10_model.r WARNING @ Sat, 11 Dec 2021 07:15:49: #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 07:15:49: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:15:49: #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 07:15:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:15:55: 2000000 INFO @ Sat, 11 Dec 2021 07:16:00: 3000000 INFO @ Sat, 11 Dec 2021 07:16:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:16:06: 4000000 INFO @ Sat, 11 Dec 2021 07:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.10_summits.bed INFO @ Sat, 11 Dec 2021 07:16:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1087 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:16:12: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:16:18: 6000000 INFO @ Sat, 11 Dec 2021 07:16:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:16:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:16:22: #1 total tags in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:16:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:16:22: #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 07:16:22: #1 tags after filtering in treatment: 6813875 INFO @ Sat, 11 Dec 2021 07:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:16:22: #1 finished! INFO @ Sat, 11 Dec 2021 07:16:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:16:23: #2 number of paired peaks: 349 WARNING @ Sat, 11 Dec 2021 07:16:23: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 11 Dec 2021 07:16:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:16:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:16:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:16:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:16:23: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:16:23: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20_model.r WARNING @ Sat, 11 Dec 2021 07:16:23: #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 07:16:23: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:16:23: #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 07:16:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:16:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:16:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689089/SRX8689089.20_summits.bed INFO @ Sat, 11 Dec 2021 07:16:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (712 records, 4 fields): 1 millis CompletedMACS2peakCalling