Job ID = 14170498 SRX = SRX8689059 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5347995 spots for SRR12174373/SRR12174373.sra Written 5347995 spots for SRR12174373/SRR12174373.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170900 ("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: 00:02:02 5347995 reads; of these: 5347995 (100.00%) were unpaired; of these: 146661 (2.74%) aligned 0 times 3703550 (69.25%) aligned exactly 1 time 1497784 (28.01%) aligned >1 times 97.26% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 258014 / 5201334 = 0.0496 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 07:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.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 07:01:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:51: 1000000 INFO @ Sat, 11 Dec 2021 07:01:57: 2000000 INFO @ Sat, 11 Dec 2021 07:02:03: 3000000 INFO @ Sat, 11 Dec 2021 07:02:09: 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 @ Sat, 11 Dec 2021 07:02:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:14: #1 total tags in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:02:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:14: #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 07:02:14: #1 tags after filtering in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:14: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:15: #2 number of paired peaks: 377 WARNING @ Sat, 11 Dec 2021 07:02:15: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:15: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:15: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:15: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:15: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:15: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:02:15: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05_model.r WARNING @ Sat, 11 Dec 2021 07:02:15: #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 07:02:15: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:02:15: #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 07:02:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.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 07:02:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:21: 1000000 INFO @ Sat, 11 Dec 2021 07:02:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:27: 2000000 INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.05_summits.bed INFO @ Sat, 11 Dec 2021 07:02:30: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1238 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:33: 3000000 INFO @ Sat, 11 Dec 2021 07:02:39: 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 @ Sat, 11 Dec 2021 07:02:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:44: #1 total tags in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:02:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:44: #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 07:02:44: #1 tags after filtering in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:44: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:44: #2 number of paired peaks: 377 WARNING @ Sat, 11 Dec 2021 07:02:44: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:44: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:44: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:44: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:44: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:44: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:02:44: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10_model.r WARNING @ Sat, 11 Dec 2021 07:02:44: #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 07:02:44: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:02:44: #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 07:02:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.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 07:02:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:51: 1000000 INFO @ Sat, 11 Dec 2021 07:02:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:56: 2000000 INFO @ Sat, 11 Dec 2021 07:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.10_summits.bed INFO @ Sat, 11 Dec 2021 07:03:00: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:03:02: 3000000 INFO @ Sat, 11 Dec 2021 07:03:08: 4000000 INFO @ Sat, 11 Dec 2021 07:03:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:03:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:03:13: #1 total tags in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:03:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:03:13: #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 07:03:13: #1 tags after filtering in treatment: 4943320 INFO @ Sat, 11 Dec 2021 07:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:03:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:03:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:03:14: #2 number of paired peaks: 377 WARNING @ Sat, 11 Dec 2021 07:03:14: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 11 Dec 2021 07:03:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:03:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:03:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:03:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:03:14: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:03:14: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20_model.r WARNING @ Sat, 11 Dec 2021 07:03:14: #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 07:03:14: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:03:14: #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 07:03:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:03:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:03:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689059/SRX8689059.20_summits.bed INFO @ Sat, 11 Dec 2021 07:03:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (641 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。