Job ID = 12265355 SRX = SRX6430371 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27502576 spots for SRR9669870/SRR9669870.sra Written 27502576 spots for SRR9669870/SRR9669870.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265527 ("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: 00:16:18 27502576 reads; of these: 27502576 (100.00%) were paired; of these: 16671501 (60.62%) aligned concordantly 0 times 6579119 (23.92%) aligned concordantly exactly 1 time 4251956 (15.46%) aligned concordantly >1 times ---- 16671501 pairs aligned concordantly 0 times; of these: 1171049 (7.02%) aligned discordantly 1 time ---- 15500452 pairs aligned 0 times concordantly or discordantly; of these: 31000904 mates make up the pairs; of these: 29839220 (96.25%) aligned 0 times 394199 (1.27%) aligned exactly 1 time 767485 (2.48%) aligned >1 times 45.75% overall alignment rate Time searching: 00:16:18 Overall time: 00:16:18 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2229419 / 11846766 = 0.1882 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.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, 03 Apr 2021 07:04:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:47: 1000000 INFO @ Sat, 03 Apr 2021 07:04:54: 2000000 INFO @ Sat, 03 Apr 2021 07:05:00: 3000000 INFO @ Sat, 03 Apr 2021 07:05:06: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.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, 03 Apr 2021 07:05:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:05:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:05:13: 5000000 INFO @ Sat, 03 Apr 2021 07:05:18: 1000000 INFO @ Sat, 03 Apr 2021 07:05:20: 6000000 INFO @ Sat, 03 Apr 2021 07:05:25: 2000000 INFO @ Sat, 03 Apr 2021 07:05:27: 7000000 INFO @ Sat, 03 Apr 2021 07:05:32: 3000000 INFO @ Sat, 03 Apr 2021 07:05:34: 8000000 INFO @ Sat, 03 Apr 2021 07:05:39: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:05:41: 9000000 INFO @ Sat, 03 Apr 2021 07:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.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, 03 Apr 2021 07:05:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:05:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:05:45: 5000000 INFO @ Sat, 03 Apr 2021 07:05:48: 1000000 INFO @ Sat, 03 Apr 2021 07:05:48: 10000000 INFO @ Sat, 03 Apr 2021 07:05:52: 6000000 INFO @ Sat, 03 Apr 2021 07:05:55: 2000000 INFO @ Sat, 03 Apr 2021 07:05:55: 11000000 INFO @ Sat, 03 Apr 2021 07:05:59: 7000000 INFO @ Sat, 03 Apr 2021 07:06:01: 3000000 INFO @ Sat, 03 Apr 2021 07:06:02: 12000000 INFO @ Sat, 03 Apr 2021 07:06:06: 8000000 INFO @ Sat, 03 Apr 2021 07:06:08: 4000000 INFO @ Sat, 03 Apr 2021 07:06:09: 13000000 INFO @ Sat, 03 Apr 2021 07:06:13: 9000000 INFO @ Sat, 03 Apr 2021 07:06:15: 5000000 INFO @ Sat, 03 Apr 2021 07:06:16: 14000000 INFO @ Sat, 03 Apr 2021 07:06:19: 10000000 INFO @ Sat, 03 Apr 2021 07:06:22: 6000000 INFO @ Sat, 03 Apr 2021 07:06:23: 15000000 INFO @ Sat, 03 Apr 2021 07:06:26: 11000000 INFO @ Sat, 03 Apr 2021 07:06:28: 7000000 INFO @ Sat, 03 Apr 2021 07:06:30: 16000000 INFO @ Sat, 03 Apr 2021 07:06:33: 12000000 INFO @ Sat, 03 Apr 2021 07:06:35: 8000000 INFO @ Sat, 03 Apr 2021 07:06:37: 17000000 INFO @ Sat, 03 Apr 2021 07:06:39: 13000000 INFO @ Sat, 03 Apr 2021 07:06:42: 9000000 INFO @ Sat, 03 Apr 2021 07:06:45: 18000000 INFO @ Sat, 03 Apr 2021 07:06:46: 14000000 INFO @ Sat, 03 Apr 2021 07:06:48: 10000000 INFO @ Sat, 03 Apr 2021 07:06:52: 19000000 INFO @ Sat, 03 Apr 2021 07:06:53: 15000000 INFO @ Sat, 03 Apr 2021 07:06:55: 11000000 INFO @ Sat, 03 Apr 2021 07:06:59: 20000000 INFO @ Sat, 03 Apr 2021 07:06:59: 16000000 INFO @ Sat, 03 Apr 2021 07:07:02: 12000000 INFO @ Sat, 03 Apr 2021 07:07:05: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:05: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:05: #1 total tags in treatment: 8646275 INFO @ Sat, 03 Apr 2021 07:07:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:05: #1 tags after filtering in treatment: 7116759 INFO @ Sat, 03 Apr 2021 07:07:05: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:07:05: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:05: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 07:07:05: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:05: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:05: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:05: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:05: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:05: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:07:05: #2 alternative fragment length(s) may be 3,56,457,531,554 bps INFO @ Sat, 03 Apr 2021 07:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05_model.r WARNING @ Sat, 03 Apr 2021 07:07:05: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:05: #2 You may need to consider one of the other alternative d(s): 3,56,457,531,554 WARNING @ Sat, 03 Apr 2021 07:07:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:06: 17000000 INFO @ Sat, 03 Apr 2021 07:07:08: 13000000 INFO @ Sat, 03 Apr 2021 07:07:13: 18000000 INFO @ Sat, 03 Apr 2021 07:07:15: 14000000 INFO @ Sat, 03 Apr 2021 07:07:19: 19000000 INFO @ Sat, 03 Apr 2021 07:07:21: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:07:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:07:26: 20000000 INFO @ Sat, 03 Apr 2021 07:07:28: 16000000 INFO @ Sat, 03 Apr 2021 07:07:30: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:30: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:30: #1 total tags in treatment: 8646275 INFO @ Sat, 03 Apr 2021 07:07:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:31: #1 tags after filtering in treatment: 7116759 INFO @ Sat, 03 Apr 2021 07:07:31: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:07:31: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.05_summits.bed INFO @ Sat, 03 Apr 2021 07:07:31: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1062 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:07:31: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 07:07:31: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:31: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:07:31: #2 alternative fragment length(s) may be 3,56,457,531,554 bps INFO @ Sat, 03 Apr 2021 07:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10_model.r WARNING @ Sat, 03 Apr 2021 07:07:31: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:31: #2 You may need to consider one of the other alternative d(s): 3,56,457,531,554 WARNING @ Sat, 03 Apr 2021 07:07:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:34: 17000000 INFO @ Sat, 03 Apr 2021 07:07:40: 18000000 INFO @ Sat, 03 Apr 2021 07:07:46: 19000000 INFO @ Sat, 03 Apr 2021 07:07:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:07:52: 20000000 INFO @ Sat, 03 Apr 2021 07:07:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:56: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:56: #1 total tags in treatment: 8646275 INFO @ Sat, 03 Apr 2021 07:07:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:56: #1 tags after filtering in treatment: 7116759 INFO @ Sat, 03 Apr 2021 07:07:56: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:07:56: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.10_summits.bed INFO @ Sat, 03 Apr 2021 07:07:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:07:57: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 07:07:57: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:57: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:57: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:57: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:57: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:57: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 07:07:57: #2 alternative fragment length(s) may be 3,56,457,531,554 bps INFO @ Sat, 03 Apr 2021 07:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20_model.r WARNING @ Sat, 03 Apr 2021 07:07:57: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:57: #2 You may need to consider one of the other alternative d(s): 3,56,457,531,554 WARNING @ Sat, 03 Apr 2021 07:07:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:08:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430371/SRX6430371.20_summits.bed INFO @ Sat, 03 Apr 2021 07:08:23: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 1 millis CompletedMACS2peakCalling