Job ID = 14170495 SRX = SRX8689056 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5343992 spots for SRR12174370/SRR12174370.sra Written 5343992 spots for SRR12174370/SRR12174370.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170898 ("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: 00:02:07 5343992 reads; of these: 5343992 (100.00%) were unpaired; of these: 115475 (2.16%) aligned 0 times 4025161 (75.32%) aligned exactly 1 time 1203356 (22.52%) aligned >1 times 97.84% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 202099 / 5228517 = 0.0387 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 07:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.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 07:01:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:44: 1000000 INFO @ Sat, 11 Dec 2021 07:01:53: 2000000 INFO @ Sat, 11 Dec 2021 07:02:01: 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 07:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.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 07:02:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:10: 4000000 INFO @ Sat, 11 Dec 2021 07:02:15: 1000000 INFO @ Sat, 11 Dec 2021 07:02:20: 5000000 INFO @ Sat, 11 Dec 2021 07:02:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:21: #1 total tags in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:02:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:21: #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 07:02:21: #1 tags after filtering in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:21: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:21: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:02:21: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:21: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:21: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:21: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:21: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:21: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:02:21: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05_model.r WARNING @ Sat, 11 Dec 2021 07:02:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:21: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:02:21: #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 07:02:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:24: 2000000 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 07:02:33: 3000000 INFO @ Sat, 11 Dec 2021 07:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.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 07:02:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:42: 4000000 INFO @ Sat, 11 Dec 2021 07:02:43: 1000000 INFO @ Sat, 11 Dec 2021 07:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.05_summits.bed INFO @ Sat, 11 Dec 2021 07:02:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1025 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:51: 2000000 INFO @ Sat, 11 Dec 2021 07:02:51: 5000000 INFO @ Sat, 11 Dec 2021 07:02:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:52: #1 total tags in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:02:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:52: #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 07:02:52: #1 tags after filtering in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:02:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:52: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:52: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:02:52: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:52: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:52: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:52: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:52: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:52: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:02:52: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10_model.r WARNING @ Sat, 11 Dec 2021 07:02:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:52: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:02:52: #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 07:02:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:03:06: 4000000 INFO @ Sat, 11 Dec 2021 07:03:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:03:14: 5000000 INFO @ Sat, 11 Dec 2021 07:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.10_summits.bed INFO @ Sat, 11 Dec 2021 07:03:14: Done! INFO @ Sat, 11 Dec 2021 07:03:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:03:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:03:14: #1 total tags in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:03:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:03:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (767 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:03:14: #1 tags after filtering in treatment: 5026418 INFO @ Sat, 11 Dec 2021 07:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:03:14: #1 finished! INFO @ Sat, 11 Dec 2021 07:03:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:03:15: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:03:15: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:03:15: start model_add_line... INFO @ Sat, 11 Dec 2021 07:03:15: start X-correlation... INFO @ Sat, 11 Dec 2021 07:03:15: end of X-cor INFO @ Sat, 11 Dec 2021 07:03:15: #2 finished! INFO @ Sat, 11 Dec 2021 07:03:15: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:03:15: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:03:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20_model.r WARNING @ Sat, 11 Dec 2021 07:03:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:03:15: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:03:15: #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 07:03:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:03:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:03:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:03:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689056/SRX8689056.20_summits.bed INFO @ Sat, 11 Dec 2021 07:03:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 2 millis CompletedMACS2peakCalling