Job ID = 14171842 SRX = SRX9008842 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17295396 spots for SRR12518314/SRR12518314.sra Written 17295396 spots for SRR12518314/SRR12518314.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172497 ("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: 00:46:53 17295396 reads; of these: 17295396 (100.00%) were paired; of these: 1690675 (9.78%) aligned concordantly 0 times 13355150 (77.22%) aligned concordantly exactly 1 time 2249571 (13.01%) aligned concordantly >1 times ---- 1690675 pairs aligned concordantly 0 times; of these: 826464 (48.88%) aligned discordantly 1 time ---- 864211 pairs aligned 0 times concordantly or discordantly; of these: 1728422 mates make up the pairs; of these: 1171797 (67.80%) aligned 0 times 305925 (17.70%) aligned exactly 1 time 250700 (14.50%) aligned >1 times 96.61% overall alignment rate Time searching: 00:46:54 Overall time: 00:46:54 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] 1206359 / 16318497 = 0.0739 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 14:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.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 14:06:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:06:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:06:43: 1000000 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 14:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.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 14:06:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:06:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:06:58: 2000000 INFO @ Sat, 11 Dec 2021 14:07:09: 1000000 INFO @ Sat, 11 Dec 2021 14:07:13: 3000000 INFO @ Sat, 11 Dec 2021 14:07:21: 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 14:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.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 14:07:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:07:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:07:29: 4000000 INFO @ Sat, 11 Dec 2021 14:07:33: 3000000 INFO @ Sat, 11 Dec 2021 14:07:41: 1000000 INFO @ Sat, 11 Dec 2021 14:07:43: 5000000 INFO @ Sat, 11 Dec 2021 14:07:46: 4000000 INFO @ Sat, 11 Dec 2021 14:07:55: 2000000 INFO @ Sat, 11 Dec 2021 14:07:58: 6000000 INFO @ Sat, 11 Dec 2021 14:07:58: 5000000 INFO @ Sat, 11 Dec 2021 14:08:10: 3000000 INFO @ Sat, 11 Dec 2021 14:08:11: 6000000 INFO @ Sat, 11 Dec 2021 14:08:12: 7000000 INFO @ Sat, 11 Dec 2021 14:08:23: 7000000 INFO @ Sat, 11 Dec 2021 14:08:24: 4000000 INFO @ Sat, 11 Dec 2021 14:08:27: 8000000 INFO @ Sat, 11 Dec 2021 14:08:35: 8000000 INFO @ Sat, 11 Dec 2021 14:08:38: 5000000 INFO @ Sat, 11 Dec 2021 14:08:42: 9000000 INFO @ Sat, 11 Dec 2021 14:08:48: 9000000 INFO @ Sat, 11 Dec 2021 14:08:53: 6000000 INFO @ Sat, 11 Dec 2021 14:08:55: 10000000 INFO @ Sat, 11 Dec 2021 14:09:01: 10000000 INFO @ Sat, 11 Dec 2021 14:09:07: 7000000 INFO @ Sat, 11 Dec 2021 14:09:09: 11000000 INFO @ Sat, 11 Dec 2021 14:09:13: 11000000 INFO @ Sat, 11 Dec 2021 14:09:21: 8000000 INFO @ Sat, 11 Dec 2021 14:09:22: 12000000 INFO @ Sat, 11 Dec 2021 14:09:26: 12000000 INFO @ Sat, 11 Dec 2021 14:09:34: 13000000 INFO @ Sat, 11 Dec 2021 14:09:35: 9000000 INFO @ Sat, 11 Dec 2021 14:09:38: 13000000 INFO @ Sat, 11 Dec 2021 14:09:47: 14000000 INFO @ Sat, 11 Dec 2021 14:09:50: 10000000 INFO @ Sat, 11 Dec 2021 14:09:51: 14000000 INFO @ Sat, 11 Dec 2021 14:09:59: 15000000 INFO @ Sat, 11 Dec 2021 14:10:03: 15000000 INFO @ Sat, 11 Dec 2021 14:10:05: 11000000 INFO @ Sat, 11 Dec 2021 14:10:12: 16000000 INFO @ Sat, 11 Dec 2021 14:10:16: 16000000 INFO @ Sat, 11 Dec 2021 14:10:19: 12000000 INFO @ Sat, 11 Dec 2021 14:10:25: 17000000 INFO @ Sat, 11 Dec 2021 14:10:28: 17000000 INFO @ Sat, 11 Dec 2021 14:10:34: 13000000 INFO @ Sat, 11 Dec 2021 14:10:37: 18000000 INFO @ Sat, 11 Dec 2021 14:10:41: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:10:49: 14000000 INFO @ Sat, 11 Dec 2021 14:10:49: 19000000 INFO @ Sat, 11 Dec 2021 14:10:53: 19000000 INFO @ Sat, 11 Dec 2021 14:11:02: 20000000 INFO @ Sat, 11 Dec 2021 14:11:03: 15000000 INFO @ Sat, 11 Dec 2021 14:11:06: 20000000 INFO @ Sat, 11 Dec 2021 14:11:14: 21000000 INFO @ Sat, 11 Dec 2021 14:11:17: 16000000 INFO @ Sat, 11 Dec 2021 14:11:18: 21000000 INFO @ Sat, 11 Dec 2021 14:11:26: 22000000 INFO @ Sat, 11 Dec 2021 14:11:30: 22000000 INFO @ Sat, 11 Dec 2021 14:11:32: 17000000 INFO @ Sat, 11 Dec 2021 14:11:39: 23000000 INFO @ Sat, 11 Dec 2021 14:11:43: 23000000 INFO @ Sat, 11 Dec 2021 14:11:46: 18000000 INFO @ Sat, 11 Dec 2021 14:11:51: 24000000 INFO @ Sat, 11 Dec 2021 14:11:55: 24000000 INFO @ Sat, 11 Dec 2021 14:12:00: 19000000 INFO @ Sat, 11 Dec 2021 14:12:04: 25000000 INFO @ Sat, 11 Dec 2021 14:12:08: 25000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:12:15: 20000000 INFO @ Sat, 11 Dec 2021 14:12:16: 26000000 INFO @ Sat, 11 Dec 2021 14:12:20: 26000000 INFO @ Sat, 11 Dec 2021 14:12:29: 27000000 INFO @ Sat, 11 Dec 2021 14:12:30: 21000000 INFO @ Sat, 11 Dec 2021 14:12:33: 27000000 INFO @ Sat, 11 Dec 2021 14:12:41: 28000000 INFO @ Sat, 11 Dec 2021 14:12:45: 28000000 INFO @ Sat, 11 Dec 2021 14:12:45: 22000000 INFO @ Sat, 11 Dec 2021 14:12:53: 29000000 INFO @ Sat, 11 Dec 2021 14:12:57: 29000000 INFO @ Sat, 11 Dec 2021 14:13:00: 23000000 INFO @ Sat, 11 Dec 2021 14:13:06: 30000000 INFO @ Sat, 11 Dec 2021 14:13:10: 30000000 INFO @ Sat, 11 Dec 2021 14:13:15: 24000000 INFO @ Sat, 11 Dec 2021 14:13:18: 31000000 INFO @ Sat, 11 Dec 2021 14:13:18: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 14:13:18: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 14:13:18: #1 total tags in treatment: 14435844 INFO @ Sat, 11 Dec 2021 14:13:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:13:18: #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 14:13:19: #1 tags after filtering in treatment: 13511723 INFO @ Sat, 11 Dec 2021 14:13:19: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:13:19: #1 finished! INFO @ Sat, 11 Dec 2021 14:13:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:13:20: #2 number of paired peaks: 712 WARNING @ Sat, 11 Dec 2021 14:13:20: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 11 Dec 2021 14:13:20: start model_add_line... INFO @ Sat, 11 Dec 2021 14:13:20: start X-correlation... INFO @ Sat, 11 Dec 2021 14:13:20: end of X-cor INFO @ Sat, 11 Dec 2021 14:13:20: #2 finished! INFO @ Sat, 11 Dec 2021 14:13:20: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 14:13:20: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 11 Dec 2021 14:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05_model.r WARNING @ Sat, 11 Dec 2021 14:13:20: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:13:20: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 11 Dec 2021 14:13:20: #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 14:13:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:13:22: 31000000 INFO @ Sat, 11 Dec 2021 14:13:22: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 14:13:22: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 14:13:22: #1 total tags in treatment: 14435844 INFO @ Sat, 11 Dec 2021 14:13:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:13:22: #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 14:13:23: #1 tags after filtering in treatment: 13511723 INFO @ Sat, 11 Dec 2021 14:13:23: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:13:23: #1 finished! INFO @ Sat, 11 Dec 2021 14:13:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:13:24: #2 number of paired peaks: 712 WARNING @ Sat, 11 Dec 2021 14:13:24: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 11 Dec 2021 14:13:24: start model_add_line... INFO @ Sat, 11 Dec 2021 14:13:24: start X-correlation... INFO @ Sat, 11 Dec 2021 14:13:24: end of X-cor INFO @ Sat, 11 Dec 2021 14:13:24: #2 finished! INFO @ Sat, 11 Dec 2021 14:13:24: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 14:13:24: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 11 Dec 2021 14:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10_model.r WARNING @ Sat, 11 Dec 2021 14:13:24: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:13:24: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 11 Dec 2021 14:13:24: #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 14:13:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:13:30: 25000000 INFO @ Sat, 11 Dec 2021 14:13:44: 26000000 INFO @ Sat, 11 Dec 2021 14:13:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:13:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:13:58: 27000000 INFO @ Sat, 11 Dec 2021 14:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.05_summits.bed INFO @ Sat, 11 Dec 2021 14:14:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6175 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.10_summits.bed INFO @ Sat, 11 Dec 2021 14:14:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4475 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:14:13: 28000000 INFO @ Sat, 11 Dec 2021 14:14:28: 29000000 INFO @ Sat, 11 Dec 2021 14:14:42: 30000000 INFO @ Sat, 11 Dec 2021 14:14:56: 31000000 INFO @ Sat, 11 Dec 2021 14:14:56: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 14:14:56: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 14:14:56: #1 total tags in treatment: 14435844 INFO @ Sat, 11 Dec 2021 14:14:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:14:56: #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 14:14:56: #1 tags after filtering in treatment: 13511723 INFO @ Sat, 11 Dec 2021 14:14:56: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:14:56: #1 finished! INFO @ Sat, 11 Dec 2021 14:14:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:14:57: #2 number of paired peaks: 712 WARNING @ Sat, 11 Dec 2021 14:14:57: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 11 Dec 2021 14:14:57: start model_add_line... INFO @ Sat, 11 Dec 2021 14:14:57: start X-correlation... INFO @ Sat, 11 Dec 2021 14:14:57: end of X-cor INFO @ Sat, 11 Dec 2021 14:14:57: #2 finished! INFO @ Sat, 11 Dec 2021 14:14:57: #2 predicted fragment length is 148 bps INFO @ Sat, 11 Dec 2021 14:14:57: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 11 Dec 2021 14:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20_model.r WARNING @ Sat, 11 Dec 2021 14:14:57: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:14:57: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sat, 11 Dec 2021 14:14:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:14:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:15:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008842/SRX9008842.20_summits.bed INFO @ Sat, 11 Dec 2021 14:15:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2434 records, 4 fields): 7 millis CompletedMACS2peakCalling