Job ID = 14168945 SRX = SRX9910781 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34843564 spots for SRR13498852/SRR13498852.sra Written 34843564 spots for SRR13498852/SRR13498852.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170084 ("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: 01:20:00 34843564 reads; of these: 34843564 (100.00%) were paired; of these: 14848620 (42.62%) aligned concordantly 0 times 12803903 (36.75%) aligned concordantly exactly 1 time 7191041 (20.64%) aligned concordantly >1 times ---- 14848620 pairs aligned concordantly 0 times; of these: 2231709 (15.03%) aligned discordantly 1 time ---- 12616911 pairs aligned 0 times concordantly or discordantly; of these: 25233822 mates make up the pairs; of these: 20275602 (80.35%) aligned 0 times 507913 (2.01%) aligned exactly 1 time 4450307 (17.64%) aligned >1 times 70.90% overall alignment rate Time searching: 01:20:01 Overall time: 01:20:01 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 36 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] 8632577 / 22065431 = 0.3912 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 23:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.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 23:41:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:41:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:41:33: 1000000 INFO @ Fri, 10 Dec 2021 23:41:40: 2000000 INFO @ Fri, 10 Dec 2021 23:41:48: 3000000 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 23:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.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 23:41:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:41:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:41:55: 4000000 INFO @ Fri, 10 Dec 2021 23:42:04: 1000000 INFO @ Fri, 10 Dec 2021 23:42:04: 5000000 INFO @ Fri, 10 Dec 2021 23:42:12: 6000000 INFO @ Fri, 10 Dec 2021 23:42:12: 2000000 INFO @ Fri, 10 Dec 2021 23:42:21: 7000000 INFO @ Fri, 10 Dec 2021 23:42:21: 3000000 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 23:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.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 23:42:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:42:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:42:29: 8000000 INFO @ Fri, 10 Dec 2021 23:42:30: 4000000 INFO @ Fri, 10 Dec 2021 23:42:34: 1000000 INFO @ Fri, 10 Dec 2021 23:42:38: 9000000 INFO @ Fri, 10 Dec 2021 23:42:38: 5000000 INFO @ Fri, 10 Dec 2021 23:42:43: 2000000 INFO @ Fri, 10 Dec 2021 23:42:47: 6000000 INFO @ Fri, 10 Dec 2021 23:42:47: 10000000 INFO @ Fri, 10 Dec 2021 23:42:51: 3000000 INFO @ Fri, 10 Dec 2021 23:42:55: 7000000 INFO @ Fri, 10 Dec 2021 23:42:56: 11000000 INFO @ Fri, 10 Dec 2021 23:43:00: 4000000 INFO @ Fri, 10 Dec 2021 23:43:04: 8000000 INFO @ Fri, 10 Dec 2021 23:43:04: 12000000 INFO @ Fri, 10 Dec 2021 23:43:09: 5000000 INFO @ Fri, 10 Dec 2021 23:43:13: 9000000 INFO @ Fri, 10 Dec 2021 23:43:13: 13000000 INFO @ Fri, 10 Dec 2021 23:43:18: 6000000 INFO @ Fri, 10 Dec 2021 23:43:21: 10000000 INFO @ Fri, 10 Dec 2021 23:43:22: 14000000 INFO @ Fri, 10 Dec 2021 23:43:27: 7000000 INFO @ Fri, 10 Dec 2021 23:43:30: 11000000 INFO @ Fri, 10 Dec 2021 23:43:30: 15000000 INFO @ Fri, 10 Dec 2021 23:43:35: 8000000 INFO @ Fri, 10 Dec 2021 23:43:39: 12000000 INFO @ Fri, 10 Dec 2021 23:43:39: 16000000 INFO @ Fri, 10 Dec 2021 23:43:44: 9000000 INFO @ Fri, 10 Dec 2021 23:43:47: 13000000 INFO @ Fri, 10 Dec 2021 23:43:48: 17000000 INFO @ Fri, 10 Dec 2021 23:43:53: 10000000 INFO @ Fri, 10 Dec 2021 23:43:56: 14000000 INFO @ Fri, 10 Dec 2021 23:43:56: 18000000 INFO @ Fri, 10 Dec 2021 23:44:02: 11000000 INFO @ Fri, 10 Dec 2021 23:44:04: 15000000 INFO @ Fri, 10 Dec 2021 23:44:05: 19000000 INFO @ Fri, 10 Dec 2021 23:44:10: 12000000 INFO @ Fri, 10 Dec 2021 23:44:13: 16000000 INFO @ Fri, 10 Dec 2021 23:44:14: 20000000 INFO @ Fri, 10 Dec 2021 23:44:19: 13000000 INFO @ Fri, 10 Dec 2021 23:44:22: 17000000 INFO @ Fri, 10 Dec 2021 23:44:22: 21000000 INFO @ Fri, 10 Dec 2021 23:44:28: 14000000 INFO @ Fri, 10 Dec 2021 23:44:30: 18000000 INFO @ Fri, 10 Dec 2021 23:44:31: 22000000 INFO @ Fri, 10 Dec 2021 23:44:36: 15000000 INFO @ Fri, 10 Dec 2021 23:44:39: 19000000 INFO @ Fri, 10 Dec 2021 23:44:39: 23000000 INFO @ Fri, 10 Dec 2021 23:44:45: 16000000 INFO @ Fri, 10 Dec 2021 23:44:47: 20000000 INFO @ Fri, 10 Dec 2021 23:44:48: 24000000 INFO @ Fri, 10 Dec 2021 23:44:54: 17000000 INFO @ Fri, 10 Dec 2021 23:44:55: 21000000 INFO @ Fri, 10 Dec 2021 23:44:56: 25000000 INFO @ Fri, 10 Dec 2021 23:45:03: 18000000 INFO @ Fri, 10 Dec 2021 23:45:04: 22000000 INFO @ Fri, 10 Dec 2021 23:45:05: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:45:11: 19000000 INFO @ Fri, 10 Dec 2021 23:45:12: 23000000 INFO @ Fri, 10 Dec 2021 23:45:14: 27000000 INFO @ Fri, 10 Dec 2021 23:45:20: 20000000 INFO @ Fri, 10 Dec 2021 23:45:21: 24000000 INFO @ Fri, 10 Dec 2021 23:45:23: 28000000 INFO @ Fri, 10 Dec 2021 23:45:29: 21000000 INFO @ Fri, 10 Dec 2021 23:45:29: 25000000 INFO @ Fri, 10 Dec 2021 23:45:31: 29000000 INFO @ Fri, 10 Dec 2021 23:45:37: 22000000 INFO @ Fri, 10 Dec 2021 23:45:38: 26000000 INFO @ Fri, 10 Dec 2021 23:45:40: 30000000 INFO @ Fri, 10 Dec 2021 23:45:46: 23000000 INFO @ Fri, 10 Dec 2021 23:45:47: 27000000 INFO @ Fri, 10 Dec 2021 23:45:49: 31000000 INFO @ Fri, 10 Dec 2021 23:45:55: 24000000 INFO @ Fri, 10 Dec 2021 23:45:56: 28000000 INFO @ Fri, 10 Dec 2021 23:45:57: 32000000 INFO @ Fri, 10 Dec 2021 23:45:59: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 23:45:59: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 23:45:59: #1 total tags in treatment: 11976479 INFO @ Fri, 10 Dec 2021 23:45:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:45:59: #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 23:45:59: #1 tags after filtering in treatment: 9729576 INFO @ Fri, 10 Dec 2021 23:45:59: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 23:45:59: #1 finished! INFO @ Fri, 10 Dec 2021 23:45:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:46:00: #2 number of paired peaks: 154 WARNING @ Fri, 10 Dec 2021 23:46:00: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 10 Dec 2021 23:46:00: start model_add_line... INFO @ Fri, 10 Dec 2021 23:46:00: start X-correlation... INFO @ Fri, 10 Dec 2021 23:46:00: end of X-cor INFO @ Fri, 10 Dec 2021 23:46:00: #2 finished! INFO @ Fri, 10 Dec 2021 23:46:00: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 23:46:00: #2 alternative fragment length(s) may be 4,180,213 bps INFO @ Fri, 10 Dec 2021 23:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05_model.r WARNING @ Fri, 10 Dec 2021 23:46:00: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:46:00: #2 You may need to consider one of the other alternative d(s): 4,180,213 WARNING @ Fri, 10 Dec 2021 23:46:00: #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 23:46:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:46:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:46:03: 25000000 INFO @ Fri, 10 Dec 2021 23:46:04: 29000000 INFO @ Fri, 10 Dec 2021 23:46:12: 26000000 INFO @ Fri, 10 Dec 2021 23:46:13: 30000000 INFO @ Fri, 10 Dec 2021 23:46:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:46:21: 27000000 INFO @ Fri, 10 Dec 2021 23:46:22: 31000000 INFO @ Fri, 10 Dec 2021 23:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.05_summits.bed INFO @ Fri, 10 Dec 2021 23:46:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2713 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:46:30: 28000000 INFO @ Fri, 10 Dec 2021 23:46:30: 32000000 INFO @ Fri, 10 Dec 2021 23:46:31: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 23:46:31: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 23:46:31: #1 total tags in treatment: 11976479 INFO @ Fri, 10 Dec 2021 23:46:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:46:31: #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 23:46:32: #1 tags after filtering in treatment: 9729576 INFO @ Fri, 10 Dec 2021 23:46:32: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 23:46:32: #1 finished! INFO @ Fri, 10 Dec 2021 23:46:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:46:32: #2 number of paired peaks: 154 WARNING @ Fri, 10 Dec 2021 23:46:32: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 10 Dec 2021 23:46:32: start model_add_line... INFO @ Fri, 10 Dec 2021 23:46:32: start X-correlation... INFO @ Fri, 10 Dec 2021 23:46:32: end of X-cor INFO @ Fri, 10 Dec 2021 23:46:32: #2 finished! INFO @ Fri, 10 Dec 2021 23:46:32: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 23:46:32: #2 alternative fragment length(s) may be 4,180,213 bps INFO @ Fri, 10 Dec 2021 23:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10_model.r WARNING @ Fri, 10 Dec 2021 23:46:32: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:46:32: #2 You may need to consider one of the other alternative d(s): 4,180,213 WARNING @ Fri, 10 Dec 2021 23:46:32: #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 23:46:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:46:38: 29000000 INFO @ Fri, 10 Dec 2021 23:46:46: 30000000 INFO @ Fri, 10 Dec 2021 23:46:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:46:54: 31000000 INFO @ Fri, 10 Dec 2021 23:47:01: 32000000 INFO @ Fri, 10 Dec 2021 23:47:02: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 23:47:02: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 23:47:02: #1 total tags in treatment: 11976479 INFO @ Fri, 10 Dec 2021 23:47:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:47:02: #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 23:47:02: #1 tags after filtering in treatment: 9729576 INFO @ Fri, 10 Dec 2021 23:47:02: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 23:47:02: #1 finished! INFO @ Fri, 10 Dec 2021 23:47:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:47:03: #2 number of paired peaks: 154 WARNING @ Fri, 10 Dec 2021 23:47:03: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 10 Dec 2021 23:47:03: start model_add_line... INFO @ Fri, 10 Dec 2021 23:47:03: start X-correlation... INFO @ Fri, 10 Dec 2021 23:47:03: end of X-cor INFO @ Fri, 10 Dec 2021 23:47:03: #2 finished! INFO @ Fri, 10 Dec 2021 23:47:03: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 23:47:03: #2 alternative fragment length(s) may be 4,180,213 bps INFO @ Fri, 10 Dec 2021 23:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20_model.r WARNING @ Fri, 10 Dec 2021 23:47:03: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:47:03: #2 You may need to consider one of the other alternative d(s): 4,180,213 WARNING @ Fri, 10 Dec 2021 23:47:03: #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 23:47:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.10_summits.bed INFO @ Fri, 10 Dec 2021 23:47:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:47:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910781/SRX9910781.20_summits.bed INFO @ Fri, 10 Dec 2021 23:47:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 1 millis CompletedMACS2peakCalling