Job ID = 14170023 SRX = SRX8556353 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30520677 spots for SRR12024963/SRR12024963.sra Written 30520677 spots for SRR12024963/SRR12024963.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170785 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:50:21 30520677 reads; of these: 30520677 (100.00%) were paired; of these: 13818438 (45.28%) aligned concordantly 0 times 9812894 (32.15%) aligned concordantly exactly 1 time 6889345 (22.57%) aligned concordantly >1 times ---- 13818438 pairs aligned concordantly 0 times; of these: 2535995 (18.35%) aligned discordantly 1 time ---- 11282443 pairs aligned 0 times concordantly or discordantly; of these: 22564886 mates make up the pairs; of these: 18609751 (82.47%) aligned 0 times 534879 (2.37%) aligned exactly 1 time 3420256 (15.16%) aligned >1 times 69.51% overall alignment rate Time searching: 01:50:22 Overall time: 01:50:22 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 32 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] 6421498 / 19023665 = 0.3376 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 07:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.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 07:01:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:43: 1000000 INFO @ Sat, 11 Dec 2021 07:01:54: 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 07:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.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 07:02:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:05: 3000000 INFO @ Sat, 11 Dec 2021 07:02:14: 1000000 INFO @ Sat, 11 Dec 2021 07:02:17: 4000000 INFO @ Sat, 11 Dec 2021 07:02:26: 2000000 INFO @ Sat, 11 Dec 2021 07:02:28: 5000000 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 07:02:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.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 07:02:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:39: 3000000 INFO @ Sat, 11 Dec 2021 07:02:40: 6000000 INFO @ Sat, 11 Dec 2021 07:02:45: 1000000 INFO @ Sat, 11 Dec 2021 07:02:52: 7000000 INFO @ Sat, 11 Dec 2021 07:02:53: 4000000 INFO @ Sat, 11 Dec 2021 07:02:59: 2000000 INFO @ Sat, 11 Dec 2021 07:03:04: 8000000 INFO @ Sat, 11 Dec 2021 07:03:06: 5000000 INFO @ Sat, 11 Dec 2021 07:03:12: 3000000 INFO @ Sat, 11 Dec 2021 07:03:16: 9000000 INFO @ Sat, 11 Dec 2021 07:03:19: 6000000 INFO @ Sat, 11 Dec 2021 07:03:26: 4000000 INFO @ Sat, 11 Dec 2021 07:03:29: 10000000 INFO @ Sat, 11 Dec 2021 07:03:33: 7000000 INFO @ Sat, 11 Dec 2021 07:03:39: 5000000 INFO @ Sat, 11 Dec 2021 07:03:41: 11000000 INFO @ Sat, 11 Dec 2021 07:03:47: 8000000 INFO @ Sat, 11 Dec 2021 07:03:52: 12000000 INFO @ Sat, 11 Dec 2021 07:03:52: 6000000 INFO @ Sat, 11 Dec 2021 07:04:02: 9000000 INFO @ Sat, 11 Dec 2021 07:04:04: 13000000 INFO @ Sat, 11 Dec 2021 07:04:06: 7000000 INFO @ Sat, 11 Dec 2021 07:04:15: 14000000 INFO @ Sat, 11 Dec 2021 07:04:15: 10000000 INFO @ Sat, 11 Dec 2021 07:04:20: 8000000 INFO @ Sat, 11 Dec 2021 07:04:27: 15000000 INFO @ Sat, 11 Dec 2021 07:04:28: 11000000 INFO @ Sat, 11 Dec 2021 07:04:33: 9000000 INFO @ Sat, 11 Dec 2021 07:04:38: 16000000 INFO @ Sat, 11 Dec 2021 07:04:41: 12000000 INFO @ Sat, 11 Dec 2021 07:04:47: 10000000 INFO @ Sat, 11 Dec 2021 07:04:50: 17000000 INFO @ Sat, 11 Dec 2021 07:04:55: 13000000 INFO @ Sat, 11 Dec 2021 07:05:00: 11000000 INFO @ Sat, 11 Dec 2021 07:05:01: 18000000 INFO @ Sat, 11 Dec 2021 07:05:08: 14000000 INFO @ Sat, 11 Dec 2021 07:05:13: 19000000 INFO @ Sat, 11 Dec 2021 07:05:14: 12000000 INFO @ Sat, 11 Dec 2021 07:05:21: 15000000 INFO @ Sat, 11 Dec 2021 07:05:24: 20000000 INFO @ Sat, 11 Dec 2021 07:05:27: 13000000 INFO @ Sat, 11 Dec 2021 07:05:34: 16000000 INFO @ Sat, 11 Dec 2021 07:05:34: 21000000 INFO @ Sat, 11 Dec 2021 07:05:40: 14000000 INFO @ Sat, 11 Dec 2021 07:05:46: 22000000 INFO @ Sat, 11 Dec 2021 07:05:46: 17000000 INFO @ Sat, 11 Dec 2021 07:05:53: 15000000 INFO @ Sat, 11 Dec 2021 07:05:57: 23000000 INFO @ Sat, 11 Dec 2021 07:05:58: 18000000 INFO @ Sat, 11 Dec 2021 07:06:05: 16000000 INFO @ Sat, 11 Dec 2021 07:06:09: 24000000 INFO @ Sat, 11 Dec 2021 07:06:11: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:06:18: 17000000 INFO @ Sat, 11 Dec 2021 07:06:20: 25000000 INFO @ Sat, 11 Dec 2021 07:06:24: 20000000 INFO @ Sat, 11 Dec 2021 07:06:31: 18000000 INFO @ Sat, 11 Dec 2021 07:06:32: 26000000 INFO @ Sat, 11 Dec 2021 07:06:37: 21000000 INFO @ Sat, 11 Dec 2021 07:06:43: 27000000 INFO @ Sat, 11 Dec 2021 07:06:44: 19000000 INFO @ Sat, 11 Dec 2021 07:06:50: 22000000 INFO @ Sat, 11 Dec 2021 07:06:54: 28000000 INFO @ Sat, 11 Dec 2021 07:06:57: 20000000 INFO @ Sat, 11 Dec 2021 07:07:03: 23000000 INFO @ Sat, 11 Dec 2021 07:07:06: 29000000 INFO @ Sat, 11 Dec 2021 07:07:10: 21000000 INFO @ Sat, 11 Dec 2021 07:07:13: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:07:13: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:07:13: #1 total tags in treatment: 10832738 INFO @ Sat, 11 Dec 2021 07:07:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:07:13: #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 07:07:13: #1 tags after filtering in treatment: 9007053 INFO @ Sat, 11 Dec 2021 07:07:13: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:07:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:07:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:07:13: #2 number of paired peaks: 243 WARNING @ Sat, 11 Dec 2021 07:07:13: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 11 Dec 2021 07:07:13: start model_add_line... INFO @ Sat, 11 Dec 2021 07:07:13: start X-correlation... INFO @ Sat, 11 Dec 2021 07:07:13: end of X-cor INFO @ Sat, 11 Dec 2021 07:07:13: #2 finished! INFO @ Sat, 11 Dec 2021 07:07:13: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:07:13: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05_model.r WARNING @ Sat, 11 Dec 2021 07:07:13: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:07:13: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:07:13: #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 07:07:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:16: 24000000 INFO @ Sat, 11 Dec 2021 07:07:22: 22000000 INFO @ Sat, 11 Dec 2021 07:07:28: 25000000 INFO @ Sat, 11 Dec 2021 07:07:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:07:35: 23000000 INFO @ Sat, 11 Dec 2021 07:07:40: 26000000 INFO @ Sat, 11 Dec 2021 07:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.05_summits.bed INFO @ Sat, 11 Dec 2021 07:07:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3414 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:07:48: 24000000 INFO @ Sat, 11 Dec 2021 07:07:54: 27000000 INFO @ Sat, 11 Dec 2021 07:08:01: 25000000 INFO @ Sat, 11 Dec 2021 07:08:07: 28000000 INFO @ Sat, 11 Dec 2021 07:08:13: 26000000 INFO @ Sat, 11 Dec 2021 07:08:19: 29000000 INFO @ Sat, 11 Dec 2021 07:08:27: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:08:27: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:08:27: #1 total tags in treatment: 10832738 INFO @ Sat, 11 Dec 2021 07:08:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:27: #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 07:08:27: #1 tags after filtering in treatment: 9007053 INFO @ Sat, 11 Dec 2021 07:08:27: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:08:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:27: 27000000 INFO @ Sat, 11 Dec 2021 07:08:28: #2 number of paired peaks: 243 WARNING @ Sat, 11 Dec 2021 07:08:28: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:28: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:08:28: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10_model.r WARNING @ Sat, 11 Dec 2021 07:08:28: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:28: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:08:28: #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 07:08:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:08:41: 28000000 INFO @ Sat, 11 Dec 2021 07:08:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:08:54: 29000000 INFO @ Sat, 11 Dec 2021 07:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.10_summits.bed INFO @ Sat, 11 Dec 2021 07:08:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:01: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:09:01: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:09:01: #1 total tags in treatment: 10832738 INFO @ Sat, 11 Dec 2021 07:09:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:01: #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 07:09:02: #1 tags after filtering in treatment: 9007053 INFO @ Sat, 11 Dec 2021 07:09:02: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:09:02: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:02: #2 number of paired peaks: 243 WARNING @ Sat, 11 Dec 2021 07:09:02: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 11 Dec 2021 07:09:02: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:02: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:02: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:02: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:02: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:09:02: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20_model.r WARNING @ Sat, 11 Dec 2021 07:09:02: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:02: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:09:02: #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 07:09:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:09:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556353/SRX8556353.20_summits.bed INFO @ Sat, 11 Dec 2021 07:09:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (675 records, 4 fields): 3 millis CompletedMACS2peakCalling