Job ID = 14168175 SRX = SRX8723983 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13686770 spots for SRR12213367/SRR12213367.sra Written 13686770 spots for SRR12213367/SRR12213367.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168986 ("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: 00:04:34 13686770 reads; of these: 13686770 (100.00%) were unpaired; of these: 1917300 (14.01%) aligned 0 times 8544417 (62.43%) aligned exactly 1 time 3225053 (23.56%) aligned >1 times 85.99% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3915561 / 11769470 = 0.3327 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 16:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.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 16:00:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:00:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:00:39: 1000000 INFO @ Fri, 10 Dec 2021 16:00:46: 2000000 INFO @ Fri, 10 Dec 2021 16:00:52: 3000000 INFO @ Fri, 10 Dec 2021 16:00:59: 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 16:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.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 16:01:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:05: 5000000 INFO @ Fri, 10 Dec 2021 16:01:08: 1000000 INFO @ Fri, 10 Dec 2021 16:01:12: 6000000 INFO @ Fri, 10 Dec 2021 16:01:15: 2000000 INFO @ Fri, 10 Dec 2021 16:01:19: 7000000 INFO @ Fri, 10 Dec 2021 16:01:21: 3000000 INFO @ Fri, 10 Dec 2021 16:01:25: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:01:25: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:01:25: #1 total tags in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:01:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:01:25: #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 16:01:25: #1 tags after filtering in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:01:25: #1 finished! INFO @ Fri, 10 Dec 2021 16:01:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:01:26: #2 number of paired peaks: 517 WARNING @ Fri, 10 Dec 2021 16:01:26: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 10 Dec 2021 16:01:26: start model_add_line... INFO @ Fri, 10 Dec 2021 16:01:26: start X-correlation... INFO @ Fri, 10 Dec 2021 16:01:26: end of X-cor INFO @ Fri, 10 Dec 2021 16:01:26: #2 finished! INFO @ Fri, 10 Dec 2021 16:01:26: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 16:01:26: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 16:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05_model.r WARNING @ Fri, 10 Dec 2021 16:01:26: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:01:26: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 16:01:26: #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 16:01:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:01:28: 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 16:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.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 16:01:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:34: 5000000 INFO @ Fri, 10 Dec 2021 16:01:39: 1000000 INFO @ Fri, 10 Dec 2021 16:01:41: 6000000 INFO @ Fri, 10 Dec 2021 16:01:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:01:47: 2000000 INFO @ Fri, 10 Dec 2021 16:01:48: 7000000 INFO @ Fri, 10 Dec 2021 16:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.05_summits.bed INFO @ Fri, 10 Dec 2021 16:01:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2292 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:01:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:01:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:01:54: #1 total tags in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:01:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:01:54: #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 16:01:54: #1 tags after filtering in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:01:54: #1 finished! INFO @ Fri, 10 Dec 2021 16:01:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:01:54: 3000000 INFO @ Fri, 10 Dec 2021 16:01:54: #2 number of paired peaks: 517 WARNING @ Fri, 10 Dec 2021 16:01:54: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 10 Dec 2021 16:01:54: start model_add_line... INFO @ Fri, 10 Dec 2021 16:01:54: start X-correlation... INFO @ Fri, 10 Dec 2021 16:01:54: end of X-cor INFO @ Fri, 10 Dec 2021 16:01:54: #2 finished! INFO @ Fri, 10 Dec 2021 16:01:54: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 16:01:54: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 16:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10_model.r WARNING @ Fri, 10 Dec 2021 16:01:54: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:01:54: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 16:01:54: #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 16:01:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:02:00: 4000000 INFO @ Fri, 10 Dec 2021 16:02:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:02:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:02:13: 6000000 INFO @ Fri, 10 Dec 2021 16:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.10_summits.bed INFO @ Fri, 10 Dec 2021 16:02:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1499 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:02:19: 7000000 INFO @ Fri, 10 Dec 2021 16:02:24: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:02:24: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:02:24: #1 total tags in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:02:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:02:24: #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 16:02:24: #1 tags after filtering in treatment: 7853909 INFO @ Fri, 10 Dec 2021 16:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:02:24: #1 finished! INFO @ Fri, 10 Dec 2021 16:02:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:02:25: #2 number of paired peaks: 517 WARNING @ Fri, 10 Dec 2021 16:02:25: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Fri, 10 Dec 2021 16:02:25: start model_add_line... INFO @ Fri, 10 Dec 2021 16:02:25: start X-correlation... INFO @ Fri, 10 Dec 2021 16:02:25: end of X-cor INFO @ Fri, 10 Dec 2021 16:02:25: #2 finished! INFO @ Fri, 10 Dec 2021 16:02:25: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 16:02:25: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 16:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20_model.r WARNING @ Fri, 10 Dec 2021 16:02:25: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:02:25: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 16:02:25: #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 16:02:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:02:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:02:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723983/SRX8723983.20_summits.bed INFO @ Fri, 10 Dec 2021 16:02:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 4 millis CompletedMACS2peakCalling