Job ID = 14170111 SRX = SRX8556259 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 46493121 spots for SRR12024633/SRR12024633.sra Written 46493121 spots for SRR12024633/SRR12024633.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170963 ("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: 01:45:07 46493121 reads; of these: 46493121 (100.00%) were paired; of these: 34381383 (73.95%) aligned concordantly 0 times 9894383 (21.28%) aligned concordantly exactly 1 time 2217355 (4.77%) aligned concordantly >1 times ---- 34381383 pairs aligned concordantly 0 times; of these: 3264941 (9.50%) aligned discordantly 1 time ---- 31116442 pairs aligned 0 times concordantly or discordantly; of these: 62232884 mates make up the pairs; of these: 59855915 (96.18%) aligned 0 times 899247 (1.44%) aligned exactly 1 time 1477722 (2.37%) aligned >1 times 35.63% overall alignment rate Time searching: 01:45:07 Overall time: 01:45:07 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_sort_core] merging from 28 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] 1256290 / 15287269 = 0.0822 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 07:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.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 07:39:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:39:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:40:02: 1000000 INFO @ Sat, 11 Dec 2021 07:40:11: 2000000 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 07:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.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 07:40:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:40:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:40:21: 3000000 INFO @ Sat, 11 Dec 2021 07:40:30: 4000000 INFO @ Sat, 11 Dec 2021 07:40:32: 1000000 INFO @ Sat, 11 Dec 2021 07:40:39: 5000000 INFO @ Sat, 11 Dec 2021 07:40:43: 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 07:40:48: 6000000 INFO @ Sat, 11 Dec 2021 07:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.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 07:40:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:40:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:40:55: 3000000 INFO @ Sat, 11 Dec 2021 07:40:58: 7000000 INFO @ Sat, 11 Dec 2021 07:41:03: 1000000 INFO @ Sat, 11 Dec 2021 07:41:07: 8000000 INFO @ Sat, 11 Dec 2021 07:41:07: 4000000 INFO @ Sat, 11 Dec 2021 07:41:16: 2000000 INFO @ Sat, 11 Dec 2021 07:41:17: 9000000 INFO @ Sat, 11 Dec 2021 07:41:19: 5000000 INFO @ Sat, 11 Dec 2021 07:41:26: 10000000 INFO @ Sat, 11 Dec 2021 07:41:28: 3000000 INFO @ Sat, 11 Dec 2021 07:41:31: 6000000 INFO @ Sat, 11 Dec 2021 07:41:36: 11000000 INFO @ Sat, 11 Dec 2021 07:41:40: 4000000 INFO @ Sat, 11 Dec 2021 07:41:44: 7000000 INFO @ Sat, 11 Dec 2021 07:41:45: 12000000 INFO @ Sat, 11 Dec 2021 07:41:52: 5000000 INFO @ Sat, 11 Dec 2021 07:41:55: 13000000 INFO @ Sat, 11 Dec 2021 07:41:57: 8000000 INFO @ Sat, 11 Dec 2021 07:42:04: 14000000 INFO @ Sat, 11 Dec 2021 07:42:04: 6000000 INFO @ Sat, 11 Dec 2021 07:42:09: 9000000 INFO @ Sat, 11 Dec 2021 07:42:13: 15000000 INFO @ Sat, 11 Dec 2021 07:42:16: 7000000 INFO @ Sat, 11 Dec 2021 07:42:21: 10000000 INFO @ Sat, 11 Dec 2021 07:42:23: 16000000 INFO @ Sat, 11 Dec 2021 07:42:29: 8000000 INFO @ Sat, 11 Dec 2021 07:42:32: 17000000 INFO @ Sat, 11 Dec 2021 07:42:34: 11000000 INFO @ Sat, 11 Dec 2021 07:42:41: 18000000 INFO @ Sat, 11 Dec 2021 07:42:41: 9000000 INFO @ Sat, 11 Dec 2021 07:42:46: 12000000 INFO @ Sat, 11 Dec 2021 07:42:50: 19000000 INFO @ Sat, 11 Dec 2021 07:42:53: 10000000 INFO @ Sat, 11 Dec 2021 07:42:59: 13000000 INFO @ Sat, 11 Dec 2021 07:43:00: 20000000 INFO @ Sat, 11 Dec 2021 07:43:06: 11000000 INFO @ Sat, 11 Dec 2021 07:43:09: 21000000 INFO @ Sat, 11 Dec 2021 07:43:11: 14000000 INFO @ Sat, 11 Dec 2021 07:43:18: 12000000 INFO @ Sat, 11 Dec 2021 07:43:18: 22000000 INFO @ Sat, 11 Dec 2021 07:43:24: 15000000 INFO @ Sat, 11 Dec 2021 07:43:28: 23000000 INFO @ Sat, 11 Dec 2021 07:43:30: 13000000 INFO @ Sat, 11 Dec 2021 07:43:36: 16000000 INFO @ Sat, 11 Dec 2021 07:43:37: 24000000 INFO @ Sat, 11 Dec 2021 07:43:42: 14000000 INFO @ Sat, 11 Dec 2021 07:43:47: 25000000 INFO @ Sat, 11 Dec 2021 07:43:48: 17000000 INFO @ Sat, 11 Dec 2021 07:43:55: 15000000 INFO @ Sat, 11 Dec 2021 07:43:57: 26000000 INFO @ Sat, 11 Dec 2021 07:44:01: 18000000 INFO @ Sat, 11 Dec 2021 07:44:06: 27000000 INFO @ Sat, 11 Dec 2021 07:44:07: 16000000 INFO @ Sat, 11 Dec 2021 07:44:13: 19000000 INFO @ Sat, 11 Dec 2021 07:44:16: 28000000 INFO @ Sat, 11 Dec 2021 07:44:19: 17000000 INFO @ Sat, 11 Dec 2021 07:44:25: 20000000 INFO @ Sat, 11 Dec 2021 07:44:25: 29000000 INFO @ Sat, 11 Dec 2021 07:44:30: 18000000 INFO @ Sat, 11 Dec 2021 07:44:35: 30000000 INFO @ Sat, 11 Dec 2021 07:44:37: 21000000 INFO @ Sat, 11 Dec 2021 07:44:41: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:44:41: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:44:41: #1 total tags in treatment: 11073436 INFO @ Sat, 11 Dec 2021 07:44:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:44:41: #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 07:44:41: #1 tags after filtering in treatment: 9450714 INFO @ Sat, 11 Dec 2021 07:44:41: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 07:44:41: #1 finished! INFO @ Sat, 11 Dec 2021 07:44:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:44:41: #2 number of paired peaks: 352 WARNING @ Sat, 11 Dec 2021 07:44:41: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 11 Dec 2021 07:44:41: start model_add_line... INFO @ Sat, 11 Dec 2021 07:44:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:44:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:44:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:44:42: #2 predicted fragment length is 202 bps INFO @ Sat, 11 Dec 2021 07:44:42: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 11 Dec 2021 07:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05_model.r WARNING @ Sat, 11 Dec 2021 07:44:42: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:44:42: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 11 Dec 2021 07:44:42: #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 07:44:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:44:43: 19000000 INFO @ Sat, 11 Dec 2021 07:44:50: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:44:55: 20000000 INFO @ Sat, 11 Dec 2021 07:45:02: 23000000 INFO @ Sat, 11 Dec 2021 07:45:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:45:06: 21000000 INFO @ Sat, 11 Dec 2021 07:45:14: 24000000 INFO @ Sat, 11 Dec 2021 07:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.05_summits.bed INFO @ Sat, 11 Dec 2021 07:45:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5349 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:45:18: 22000000 INFO @ Sat, 11 Dec 2021 07:45:26: 25000000 INFO @ Sat, 11 Dec 2021 07:45:29: 23000000 INFO @ Sat, 11 Dec 2021 07:45:38: 26000000 INFO @ Sat, 11 Dec 2021 07:45:41: 24000000 INFO @ Sat, 11 Dec 2021 07:45:51: 27000000 INFO @ Sat, 11 Dec 2021 07:45:53: 25000000 INFO @ Sat, 11 Dec 2021 07:46:02: 28000000 INFO @ Sat, 11 Dec 2021 07:46:05: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:46:15: 29000000 INFO @ Sat, 11 Dec 2021 07:46:18: 27000000 INFO @ Sat, 11 Dec 2021 07:46:26: 30000000 INFO @ Sat, 11 Dec 2021 07:46:30: 28000000 INFO @ Sat, 11 Dec 2021 07:46:33: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:46:33: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:46:33: #1 total tags in treatment: 11073436 INFO @ Sat, 11 Dec 2021 07:46:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:46:33: #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 07:46:34: #1 tags after filtering in treatment: 9450714 INFO @ Sat, 11 Dec 2021 07:46:34: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 07:46:34: #1 finished! INFO @ Sat, 11 Dec 2021 07:46:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:46:34: #2 number of paired peaks: 352 WARNING @ Sat, 11 Dec 2021 07:46:34: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 11 Dec 2021 07:46:34: start model_add_line... INFO @ Sat, 11 Dec 2021 07:46:35: start X-correlation... INFO @ Sat, 11 Dec 2021 07:46:35: end of X-cor INFO @ Sat, 11 Dec 2021 07:46:35: #2 finished! INFO @ Sat, 11 Dec 2021 07:46:35: #2 predicted fragment length is 202 bps INFO @ Sat, 11 Dec 2021 07:46:35: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 11 Dec 2021 07:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10_model.r WARNING @ Sat, 11 Dec 2021 07:46:35: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:46:35: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 11 Dec 2021 07:46:35: #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 07:46:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:46:42: 29000000 INFO @ Sat, 11 Dec 2021 07:46:54: 30000000 INFO @ Sat, 11 Dec 2021 07:46:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:47:01: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:47:01: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:47:01: #1 total tags in treatment: 11073436 INFO @ Sat, 11 Dec 2021 07:47:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:47:01: #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 07:47:01: #1 tags after filtering in treatment: 9450714 INFO @ Sat, 11 Dec 2021 07:47:01: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 07:47:01: #1 finished! INFO @ Sat, 11 Dec 2021 07:47:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:47:02: #2 number of paired peaks: 352 WARNING @ Sat, 11 Dec 2021 07:47:02: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 11 Dec 2021 07:47:02: start model_add_line... INFO @ Sat, 11 Dec 2021 07:47:02: start X-correlation... INFO @ Sat, 11 Dec 2021 07:47:02: end of X-cor INFO @ Sat, 11 Dec 2021 07:47:02: #2 finished! INFO @ Sat, 11 Dec 2021 07:47:02: #2 predicted fragment length is 202 bps INFO @ Sat, 11 Dec 2021 07:47:02: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 11 Dec 2021 07:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20_model.r WARNING @ Sat, 11 Dec 2021 07:47:02: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:47:02: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 11 Dec 2021 07:47:02: #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 07:47:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.10_summits.bed INFO @ Sat, 11 Dec 2021 07:47:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:47:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:47:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:47:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:47:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556259/SRX8556259.20_summits.bed INFO @ Sat, 11 Dec 2021 07:47:36: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (682 records, 4 fields): 4 millis CompletedMACS2peakCalling