Job ID = 14171312 SRX = SRX9986143 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22180523 spots for SRR13591506/SRR13591506.sra Written 22180523 spots for SRR13591506/SRR13591506.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171781 ("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: 00:09:04 22180523 reads; of these: 22180523 (100.00%) were unpaired; of these: 964659 (4.35%) aligned 0 times 11260115 (50.77%) aligned exactly 1 time 9955749 (44.89%) aligned >1 times 95.65% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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 12 files... [bam_rmdupse_core] 6253041 / 21215864 = 0.2947 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 11:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.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 11:24:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:24:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:24:10: 1000000 INFO @ Sat, 11 Dec 2021 11:24:16: 2000000 INFO @ Sat, 11 Dec 2021 11:24:21: 3000000 INFO @ Sat, 11 Dec 2021 11:24:27: 4000000 INFO @ Sat, 11 Dec 2021 11:24:33: 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 11:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.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 11:24:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:24:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:24:39: 6000000 INFO @ Sat, 11 Dec 2021 11:24:42: 1000000 INFO @ Sat, 11 Dec 2021 11:24:46: 7000000 INFO @ Sat, 11 Dec 2021 11:24:50: 2000000 INFO @ Sat, 11 Dec 2021 11:24:52: 8000000 INFO @ Sat, 11 Dec 2021 11:24:57: 3000000 INFO @ Sat, 11 Dec 2021 11:24:59: 9000000 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 11:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.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 11:25:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:25:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:25:05: 4000000 INFO @ Sat, 11 Dec 2021 11:25:06: 10000000 INFO @ Sat, 11 Dec 2021 11:25:12: 1000000 INFO @ Sat, 11 Dec 2021 11:25:13: 11000000 INFO @ Sat, 11 Dec 2021 11:25:13: 5000000 INFO @ Sat, 11 Dec 2021 11:25:20: 12000000 INFO @ Sat, 11 Dec 2021 11:25:20: 2000000 INFO @ Sat, 11 Dec 2021 11:25:20: 6000000 INFO @ Sat, 11 Dec 2021 11:25:27: 13000000 INFO @ Sat, 11 Dec 2021 11:25:28: 3000000 INFO @ Sat, 11 Dec 2021 11:25:28: 7000000 INFO @ Sat, 11 Dec 2021 11:25:33: 14000000 INFO @ Sat, 11 Dec 2021 11:25:35: 8000000 INFO @ Sat, 11 Dec 2021 11:25:36: 4000000 INFO @ Sat, 11 Dec 2021 11:25:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:25:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:25:40: #1 total tags in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:25:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:25:40: #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 11:25:40: #1 tags after filtering in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:25:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:25:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:25:41: #2 number of paired peaks: 479 WARNING @ Sat, 11 Dec 2021 11:25:41: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 11 Dec 2021 11:25:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:25:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:25:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:25:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:25:41: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 11:25:41: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 11 Dec 2021 11:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05_model.r WARNING @ Sat, 11 Dec 2021 11:25:41: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:25:41: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 11 Dec 2021 11:25:41: #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 11:25:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:25:43: 9000000 INFO @ Sat, 11 Dec 2021 11:25:43: 5000000 INFO @ Sat, 11 Dec 2021 11:25:50: 10000000 INFO @ Sat, 11 Dec 2021 11:25:51: 6000000 INFO @ Sat, 11 Dec 2021 11:25:58: 11000000 INFO @ Sat, 11 Dec 2021 11:25:58: 7000000 INFO @ Sat, 11 Dec 2021 11:26:05: 12000000 INFO @ Sat, 11 Dec 2021 11:26:06: 8000000 INFO @ Sat, 11 Dec 2021 11:26:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:26:12: 13000000 INFO @ Sat, 11 Dec 2021 11:26:13: 9000000 INFO @ Sat, 11 Dec 2021 11:26:20: 14000000 INFO @ Sat, 11 Dec 2021 11:26:20: 10000000 INFO @ Sat, 11 Dec 2021 11:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.05_summits.bed INFO @ Sat, 11 Dec 2021 11:26:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3087 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:26:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:26:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:26:27: #1 total tags in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:26:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:27: #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 11:26:27: #1 tags after filtering in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:27: 11000000 INFO @ Sat, 11 Dec 2021 11:26:28: #2 number of paired peaks: 479 WARNING @ Sat, 11 Dec 2021 11:26:28: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 11 Dec 2021 11:26:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:28: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 11:26:28: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 11 Dec 2021 11:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10_model.r WARNING @ Sat, 11 Dec 2021 11:26:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:26:28: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 11 Dec 2021 11:26:28: #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 11:26:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:34: 12000000 INFO @ Sat, 11 Dec 2021 11:26:41: 13000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:26:48: 14000000 INFO @ Sat, 11 Dec 2021 11:26:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:26:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:26:54: #1 total tags in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:26:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:54: #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 11:26:54: #1 tags after filtering in treatment: 14962823 INFO @ Sat, 11 Dec 2021 11:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:54: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:55: #2 number of paired peaks: 479 WARNING @ Sat, 11 Dec 2021 11:26:55: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 11 Dec 2021 11:26:55: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:55: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:55: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:55: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:55: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 11:26:55: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 11 Dec 2021 11:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20_model.r WARNING @ Sat, 11 Dec 2021 11:26:55: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:26:55: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 11 Dec 2021 11:26:55: #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 11:26:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.10_summits.bed INFO @ Sat, 11 Dec 2021 11:27:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2079 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:27:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986143/SRX9986143.20_summits.bed INFO @ Sat, 11 Dec 2021 11:27:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 2 millis CompletedMACS2peakCalling