Job ID = 12266671 SRX = SRX8174034 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16560258 spots for SRR11607688/SRR11607688.sra Written 16560258 spots for SRR11607688/SRR11607688.sra Read 7418639 spots for SRR11607689/SRR11607689.sra Written 7418639 spots for SRR11607689/SRR11607689.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267082 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:14 23978897 reads; of these: 23978897 (100.00%) were paired; of these: 2182229 (9.10%) aligned concordantly 0 times 12159215 (50.71%) aligned concordantly exactly 1 time 9637453 (40.19%) aligned concordantly >1 times ---- 2182229 pairs aligned concordantly 0 times; of these: 716789 (32.85%) aligned discordantly 1 time ---- 1465440 pairs aligned 0 times concordantly or discordantly; of these: 2930880 mates make up the pairs; of these: 1646149 (56.17%) aligned 0 times 505159 (17.24%) aligned exactly 1 time 779572 (26.60%) aligned >1 times 96.57% overall alignment rate Time searching: 00:29:15 Overall time: 00:29:15 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 16 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] 6263884 / 22328285 = 0.2805 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 09:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.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 09:45:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:45:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:45:50: 1000000 INFO @ Sat, 03 Apr 2021 09:45:55: 2000000 INFO @ Sat, 03 Apr 2021 09:46:00: 3000000 INFO @ Sat, 03 Apr 2021 09:46:05: 4000000 INFO @ Sat, 03 Apr 2021 09:46:10: 5000000 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 09:46:15: 6000000 INFO @ Sat, 03 Apr 2021 09:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.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 09:46:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:20: 7000000 INFO @ Sat, 03 Apr 2021 09:46:20: 1000000 INFO @ Sat, 03 Apr 2021 09:46:25: 8000000 INFO @ Sat, 03 Apr 2021 09:46:25: 2000000 INFO @ Sat, 03 Apr 2021 09:46:30: 9000000 INFO @ Sat, 03 Apr 2021 09:46:30: 3000000 INFO @ Sat, 03 Apr 2021 09:46:35: 10000000 INFO @ Sat, 03 Apr 2021 09:46:36: 4000000 INFO @ Sat, 03 Apr 2021 09:46:41: 11000000 INFO @ Sat, 03 Apr 2021 09:46:41: 5000000 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 09:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.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 09:46:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:46: 12000000 INFO @ Sat, 03 Apr 2021 09:46:46: 6000000 INFO @ Sat, 03 Apr 2021 09:46:51: 1000000 INFO @ Sat, 03 Apr 2021 09:46:51: 13000000 INFO @ Sat, 03 Apr 2021 09:46:51: 7000000 INFO @ Sat, 03 Apr 2021 09:46:57: 14000000 INFO @ Sat, 03 Apr 2021 09:46:57: 2000000 INFO @ Sat, 03 Apr 2021 09:46:57: 8000000 INFO @ Sat, 03 Apr 2021 09:47:02: 15000000 INFO @ Sat, 03 Apr 2021 09:47:02: 9000000 INFO @ Sat, 03 Apr 2021 09:47:02: 3000000 INFO @ Sat, 03 Apr 2021 09:47:07: 16000000 INFO @ Sat, 03 Apr 2021 09:47:07: 10000000 INFO @ Sat, 03 Apr 2021 09:47:08: 4000000 INFO @ Sat, 03 Apr 2021 09:47:13: 17000000 INFO @ Sat, 03 Apr 2021 09:47:13: 11000000 INFO @ Sat, 03 Apr 2021 09:47:14: 5000000 INFO @ Sat, 03 Apr 2021 09:47:18: 18000000 INFO @ Sat, 03 Apr 2021 09:47:18: 12000000 INFO @ Sat, 03 Apr 2021 09:47:20: 6000000 INFO @ Sat, 03 Apr 2021 09:47:23: 19000000 INFO @ Sat, 03 Apr 2021 09:47:23: 13000000 INFO @ Sat, 03 Apr 2021 09:47:26: 7000000 INFO @ Sat, 03 Apr 2021 09:47:29: 20000000 INFO @ Sat, 03 Apr 2021 09:47:29: 14000000 INFO @ Sat, 03 Apr 2021 09:47:32: 8000000 INFO @ Sat, 03 Apr 2021 09:47:34: 21000000 INFO @ Sat, 03 Apr 2021 09:47:34: 15000000 INFO @ Sat, 03 Apr 2021 09:47:38: 9000000 INFO @ Sat, 03 Apr 2021 09:47:39: 22000000 INFO @ Sat, 03 Apr 2021 09:47:39: 16000000 INFO @ Sat, 03 Apr 2021 09:47:44: 10000000 INFO @ Sat, 03 Apr 2021 09:47:45: 23000000 INFO @ Sat, 03 Apr 2021 09:47:45: 17000000 INFO @ Sat, 03 Apr 2021 09:47:49: 11000000 INFO @ Sat, 03 Apr 2021 09:47:50: 24000000 INFO @ Sat, 03 Apr 2021 09:47:50: 18000000 INFO @ Sat, 03 Apr 2021 09:47:55: 12000000 INFO @ Sat, 03 Apr 2021 09:47:55: 25000000 INFO @ Sat, 03 Apr 2021 09:47:55: 19000000 INFO @ Sat, 03 Apr 2021 09:48:01: 26000000 INFO @ Sat, 03 Apr 2021 09:48:01: 20000000 INFO @ Sat, 03 Apr 2021 09:48:01: 13000000 INFO @ Sat, 03 Apr 2021 09:48:06: 27000000 INFO @ Sat, 03 Apr 2021 09:48:06: 21000000 INFO @ Sat, 03 Apr 2021 09:48:07: 14000000 INFO @ Sat, 03 Apr 2021 09:48:11: 28000000 INFO @ Sat, 03 Apr 2021 09:48:12: 22000000 INFO @ Sat, 03 Apr 2021 09:48:13: 15000000 INFO @ Sat, 03 Apr 2021 09:48:17: 29000000 INFO @ Sat, 03 Apr 2021 09:48:17: 23000000 INFO @ Sat, 03 Apr 2021 09:48:18: 16000000 INFO @ Sat, 03 Apr 2021 09:48:22: 30000000 INFO @ Sat, 03 Apr 2021 09:48:22: 24000000 INFO @ Sat, 03 Apr 2021 09:48:24: 17000000 INFO @ Sat, 03 Apr 2021 09:48:28: 25000000 INFO @ Sat, 03 Apr 2021 09:48:28: 31000000 INFO @ Sat, 03 Apr 2021 09:48:30: 18000000 INFO @ Sat, 03 Apr 2021 09:48:33: 26000000 INFO @ Sat, 03 Apr 2021 09:48:33: 32000000 INFO @ Sat, 03 Apr 2021 09:48:36: 19000000 INFO @ Sat, 03 Apr 2021 09:48:38: 27000000 INFO @ Sat, 03 Apr 2021 09:48:38: 33000000 INFO @ Sat, 03 Apr 2021 09:48:42: 20000000 INFO @ Sat, 03 Apr 2021 09:48:43: #1 tag size is determined as 39 bps INFO @ Sat, 03 Apr 2021 09:48:43: #1 tag size = 39 INFO @ Sat, 03 Apr 2021 09:48:43: #1 total tags in treatment: 15559266 INFO @ Sat, 03 Apr 2021 09:48:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:48:43: #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 09:48:43: #1 tags after filtering in treatment: 11583922 INFO @ Sat, 03 Apr 2021 09:48:43: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 09:48:43: #1 finished! INFO @ Sat, 03 Apr 2021 09:48:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:48:43: 28000000 INFO @ Sat, 03 Apr 2021 09:48:44: #2 number of paired peaks: 878 WARNING @ Sat, 03 Apr 2021 09:48:44: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sat, 03 Apr 2021 09:48:44: start model_add_line... INFO @ Sat, 03 Apr 2021 09:48:44: start X-correlation... INFO @ Sat, 03 Apr 2021 09:48:44: end of X-cor INFO @ Sat, 03 Apr 2021 09:48:44: #2 finished! INFO @ Sat, 03 Apr 2021 09:48:44: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 09:48:44: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sat, 03 Apr 2021 09:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05_model.r WARNING @ Sat, 03 Apr 2021 09:48:44: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:48:44: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sat, 03 Apr 2021 09:48:44: #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 09:48:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:48:48: 21000000 INFO @ Sat, 03 Apr 2021 09:48:49: 29000000 INFO @ Sat, 03 Apr 2021 09:48:53: 22000000 INFO @ Sat, 03 Apr 2021 09:48:54: 30000000 INFO @ Sat, 03 Apr 2021 09:48:59: 31000000 INFO @ Sat, 03 Apr 2021 09:48:59: 23000000 INFO @ Sat, 03 Apr 2021 09:49:05: 32000000 INFO @ Sat, 03 Apr 2021 09:49:05: 24000000 INFO @ Sat, 03 Apr 2021 09:49:10: 33000000 INFO @ Sat, 03 Apr 2021 09:49:11: 25000000 INFO @ Sat, 03 Apr 2021 09:49:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:49:14: #1 tag size is determined as 39 bps INFO @ Sat, 03 Apr 2021 09:49:14: #1 tag size = 39 INFO @ Sat, 03 Apr 2021 09:49:14: #1 total tags in treatment: 15559266 INFO @ Sat, 03 Apr 2021 09:49:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:49:14: #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 09:49:15: #1 tags after filtering in treatment: 11583922 INFO @ Sat, 03 Apr 2021 09:49:15: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 09:49:15: #1 finished! INFO @ Sat, 03 Apr 2021 09:49:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:49:16: #2 number of paired peaks: 878 WARNING @ Sat, 03 Apr 2021 09:49:16: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sat, 03 Apr 2021 09:49:16: start model_add_line... INFO @ Sat, 03 Apr 2021 09:49:16: start X-correlation... INFO @ Sat, 03 Apr 2021 09:49:16: end of X-cor INFO @ Sat, 03 Apr 2021 09:49:16: #2 finished! INFO @ Sat, 03 Apr 2021 09:49:16: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 09:49:16: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sat, 03 Apr 2021 09:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10_model.r WARNING @ Sat, 03 Apr 2021 09:49:16: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:49:16: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sat, 03 Apr 2021 09:49:16: #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 09:49:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:49:16: 26000000 INFO @ Sat, 03 Apr 2021 09:49:22: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:49:27: 28000000 INFO @ Sat, 03 Apr 2021 09:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.05_summits.bed INFO @ Sat, 03 Apr 2021 09:49:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12635 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:49:33: 29000000 INFO @ Sat, 03 Apr 2021 09:49:38: 30000000 INFO @ Sat, 03 Apr 2021 09:49:44: 31000000 INFO @ Sat, 03 Apr 2021 09:49:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:49:49: 32000000 INFO @ Sat, 03 Apr 2021 09:49:55: 33000000 INFO @ Sat, 03 Apr 2021 09:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.10_summits.bed INFO @ Sat, 03 Apr 2021 09:50:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4152 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:50:00: #1 tag size is determined as 39 bps INFO @ Sat, 03 Apr 2021 09:50:00: #1 tag size = 39 INFO @ Sat, 03 Apr 2021 09:50:00: #1 total tags in treatment: 15559266 INFO @ Sat, 03 Apr 2021 09:50:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:50:00: #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 09:50:00: #1 tags after filtering in treatment: 11583922 INFO @ Sat, 03 Apr 2021 09:50:00: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 09:50:00: #1 finished! INFO @ Sat, 03 Apr 2021 09:50:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:50:01: #2 number of paired peaks: 878 WARNING @ Sat, 03 Apr 2021 09:50:01: Fewer paired peaks (878) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 878 pairs to build model! INFO @ Sat, 03 Apr 2021 09:50:01: start model_add_line... INFO @ Sat, 03 Apr 2021 09:50:01: start X-correlation... INFO @ Sat, 03 Apr 2021 09:50:01: end of X-cor INFO @ Sat, 03 Apr 2021 09:50:01: #2 finished! INFO @ Sat, 03 Apr 2021 09:50:01: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 09:50:01: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sat, 03 Apr 2021 09:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20_model.r WARNING @ Sat, 03 Apr 2021 09:50:01: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:50:01: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sat, 03 Apr 2021 09:50:01: #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 09:50:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:50:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:50:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174034/SRX8174034.20_summits.bed INFO @ Sat, 03 Apr 2021 09:50:45: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (537 records, 4 fields): 2 millis CompletedMACS2peakCalling