Job ID = 14171786 SRX = SRX9008835 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17874254 spots for SRR12518307/SRR12518307.sra Written 17874254 spots for SRR12518307/SRR12518307.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172375 ("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: 00:33:59 17874254 reads; of these: 17874254 (100.00%) were paired; of these: 3131512 (17.52%) aligned concordantly 0 times 12085681 (67.62%) aligned concordantly exactly 1 time 2657061 (14.87%) aligned concordantly >1 times ---- 3131512 pairs aligned concordantly 0 times; of these: 1534302 (49.00%) aligned discordantly 1 time ---- 1597210 pairs aligned 0 times concordantly or discordantly; of these: 3194420 mates make up the pairs; of these: 2259606 (70.74%) aligned 0 times 350794 (10.98%) aligned exactly 1 time 584020 (18.28%) aligned >1 times 93.68% overall alignment rate Time searching: 00:33:59 Overall time: 00:33:59 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] 997829 / 16131020 = 0.0619 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 13:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.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 13:34:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:34:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:34:51: 1000000 INFO @ Sat, 11 Dec 2021 13:34:58: 2000000 INFO @ Sat, 11 Dec 2021 13:35:04: 3000000 INFO @ Sat, 11 Dec 2021 13:35:10: 4000000 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 13:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.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 13:35:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:35:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:35:17: 5000000 INFO @ Sat, 11 Dec 2021 13:35:22: 1000000 INFO @ Sat, 11 Dec 2021 13:35:23: 6000000 INFO @ Sat, 11 Dec 2021 13:35:28: 2000000 INFO @ Sat, 11 Dec 2021 13:35:30: 7000000 INFO @ Sat, 11 Dec 2021 13:35:35: 3000000 INFO @ Sat, 11 Dec 2021 13:35:37: 8000000 INFO @ Sat, 11 Dec 2021 13:35:42: 4000000 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 13:35:43: 9000000 INFO @ Sat, 11 Dec 2021 13:35:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.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 13:35:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:35:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:35:49: 5000000 INFO @ Sat, 11 Dec 2021 13:35:50: 10000000 INFO @ Sat, 11 Dec 2021 13:35:52: 1000000 INFO @ Sat, 11 Dec 2021 13:35:56: 6000000 INFO @ Sat, 11 Dec 2021 13:35:56: 11000000 INFO @ Sat, 11 Dec 2021 13:35:58: 2000000 INFO @ Sat, 11 Dec 2021 13:36:02: 7000000 INFO @ Sat, 11 Dec 2021 13:36:03: 12000000 INFO @ Sat, 11 Dec 2021 13:36:05: 3000000 INFO @ Sat, 11 Dec 2021 13:36:09: 8000000 INFO @ Sat, 11 Dec 2021 13:36:09: 13000000 INFO @ Sat, 11 Dec 2021 13:36:12: 4000000 INFO @ Sat, 11 Dec 2021 13:36:16: 14000000 INFO @ Sat, 11 Dec 2021 13:36:16: 9000000 INFO @ Sat, 11 Dec 2021 13:36:18: 5000000 INFO @ Sat, 11 Dec 2021 13:36:22: 15000000 INFO @ Sat, 11 Dec 2021 13:36:23: 10000000 INFO @ Sat, 11 Dec 2021 13:36:25: 6000000 INFO @ Sat, 11 Dec 2021 13:36:29: 16000000 INFO @ Sat, 11 Dec 2021 13:36:29: 11000000 INFO @ Sat, 11 Dec 2021 13:36:32: 7000000 INFO @ Sat, 11 Dec 2021 13:36:35: 17000000 INFO @ Sat, 11 Dec 2021 13:36:36: 12000000 INFO @ Sat, 11 Dec 2021 13:36:38: 8000000 INFO @ Sat, 11 Dec 2021 13:36:41: 18000000 INFO @ Sat, 11 Dec 2021 13:36:43: 13000000 INFO @ Sat, 11 Dec 2021 13:36:45: 9000000 INFO @ Sat, 11 Dec 2021 13:36:48: 19000000 INFO @ Sat, 11 Dec 2021 13:36:50: 14000000 INFO @ Sat, 11 Dec 2021 13:36:52: 10000000 INFO @ Sat, 11 Dec 2021 13:36:54: 20000000 INFO @ Sat, 11 Dec 2021 13:36:56: 15000000 INFO @ Sat, 11 Dec 2021 13:36:58: 11000000 INFO @ Sat, 11 Dec 2021 13:37:01: 21000000 INFO @ Sat, 11 Dec 2021 13:37:03: 16000000 INFO @ Sat, 11 Dec 2021 13:37:05: 12000000 INFO @ Sat, 11 Dec 2021 13:37:07: 22000000 INFO @ Sat, 11 Dec 2021 13:37:10: 17000000 INFO @ Sat, 11 Dec 2021 13:37:12: 13000000 INFO @ Sat, 11 Dec 2021 13:37:14: 23000000 INFO @ Sat, 11 Dec 2021 13:37:16: 18000000 INFO @ Sat, 11 Dec 2021 13:37:18: 14000000 INFO @ Sat, 11 Dec 2021 13:37:20: 24000000 INFO @ Sat, 11 Dec 2021 13:37:23: 19000000 INFO @ Sat, 11 Dec 2021 13:37:25: 15000000 INFO @ Sat, 11 Dec 2021 13:37:27: 25000000 INFO @ Sat, 11 Dec 2021 13:37:29: 20000000 INFO @ Sat, 11 Dec 2021 13:37:31: 16000000 INFO @ Sat, 11 Dec 2021 13:37:33: 26000000 INFO @ Sat, 11 Dec 2021 13:37:36: 21000000 INFO @ Sat, 11 Dec 2021 13:37:38: 17000000 INFO @ Sat, 11 Dec 2021 13:37:40: 27000000 INFO @ Sat, 11 Dec 2021 13:37:42: 22000000 INFO @ Sat, 11 Dec 2021 13:37:44: 18000000 INFO @ Sat, 11 Dec 2021 13:37:46: 28000000 INFO @ Sat, 11 Dec 2021 13:37:48: 23000000 INFO @ Sat, 11 Dec 2021 13:37:50: 19000000 INFO @ Sat, 11 Dec 2021 13:37:53: 29000000 INFO @ Sat, 11 Dec 2021 13:37:55: 24000000 INFO @ Sat, 11 Dec 2021 13:37:57: 20000000 INFO @ Sat, 11 Dec 2021 13:37:59: 30000000 INFO @ Sat, 11 Dec 2021 13:38:02: 25000000 INFO @ Sat, 11 Dec 2021 13:38:03: 21000000 INFO @ Sat, 11 Dec 2021 13:38:06: 31000000 INFO @ Sat, 11 Dec 2021 13:38:09: 26000000 INFO @ Sat, 11 Dec 2021 13:38:09: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:38:09: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:38:09: #1 total tags in treatment: 13815495 INFO @ Sat, 11 Dec 2021 13:38:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:38:09: #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 13:38:10: #1 tags after filtering in treatment: 13329989 INFO @ Sat, 11 Dec 2021 13:38:10: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:38:10: #1 finished! INFO @ Sat, 11 Dec 2021 13:38:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:38:10: 22000000 INFO @ Sat, 11 Dec 2021 13:38:10: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 13:38:10: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 13:38:10: start model_add_line... INFO @ Sat, 11 Dec 2021 13:38:10: start X-correlation... INFO @ Sat, 11 Dec 2021 13:38:10: end of X-cor INFO @ Sat, 11 Dec 2021 13:38:10: #2 finished! INFO @ Sat, 11 Dec 2021 13:38:10: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 13:38:10: #2 alternative fragment length(s) may be 2,152,173,185,553 bps INFO @ Sat, 11 Dec 2021 13:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05_model.r WARNING @ Sat, 11 Dec 2021 13:38:10: #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 13:38:10: #2 You may need to consider one of the other alternative d(s): 2,152,173,185,553 WARNING @ Sat, 11 Dec 2021 13:38:10: #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 13:38:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:38:15: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:38:16: 23000000 INFO @ Sat, 11 Dec 2021 13:38:22: 28000000 INFO @ Sat, 11 Dec 2021 13:38:23: 24000000 INFO @ Sat, 11 Dec 2021 13:38:29: 29000000 INFO @ Sat, 11 Dec 2021 13:38:30: 25000000 INFO @ Sat, 11 Dec 2021 13:38:35: 30000000 INFO @ Sat, 11 Dec 2021 13:38:36: 26000000 INFO @ Sat, 11 Dec 2021 13:38:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:38:42: 31000000 INFO @ Sat, 11 Dec 2021 13:38:43: 27000000 INFO @ Sat, 11 Dec 2021 13:38:45: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:38:45: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:38:45: #1 total tags in treatment: 13815495 INFO @ Sat, 11 Dec 2021 13:38:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:38:45: #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 13:38:45: #1 tags after filtering in treatment: 13329989 INFO @ Sat, 11 Dec 2021 13:38:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:38:45: #1 finished! INFO @ Sat, 11 Dec 2021 13:38:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:38:46: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 13:38:46: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 13:38:46: start model_add_line... INFO @ Sat, 11 Dec 2021 13:38:46: start X-correlation... INFO @ Sat, 11 Dec 2021 13:38:46: end of X-cor INFO @ Sat, 11 Dec 2021 13:38:46: #2 finished! INFO @ Sat, 11 Dec 2021 13:38:46: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 13:38:46: #2 alternative fragment length(s) may be 2,152,173,185,553 bps INFO @ Sat, 11 Dec 2021 13:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10_model.r WARNING @ Sat, 11 Dec 2021 13:38:46: #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 13:38:46: #2 You may need to consider one of the other alternative d(s): 2,152,173,185,553 WARNING @ Sat, 11 Dec 2021 13:38:46: #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 13:38:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:38:49: 28000000 INFO @ Sat, 11 Dec 2021 13:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.05_summits.bed INFO @ Sat, 11 Dec 2021 13:38:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:38:56: 29000000 INFO @ Sat, 11 Dec 2021 13:39:02: 30000000 INFO @ Sat, 11 Dec 2021 13:39:08: 31000000 INFO @ Sat, 11 Dec 2021 13:39:12: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:39:12: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:39:12: #1 total tags in treatment: 13815495 INFO @ Sat, 11 Dec 2021 13:39:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:39:12: #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 13:39:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:39:12: #1 tags after filtering in treatment: 13329989 INFO @ Sat, 11 Dec 2021 13:39:12: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 13:39:12: #1 finished! INFO @ Sat, 11 Dec 2021 13:39:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:39:13: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 13:39:13: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 13:39:13: start model_add_line... INFO @ Sat, 11 Dec 2021 13:39:13: start X-correlation... INFO @ Sat, 11 Dec 2021 13:39:13: end of X-cor INFO @ Sat, 11 Dec 2021 13:39:13: #2 finished! INFO @ Sat, 11 Dec 2021 13:39:13: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 13:39:13: #2 alternative fragment length(s) may be 2,152,173,185,553 bps INFO @ Sat, 11 Dec 2021 13:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20_model.r WARNING @ Sat, 11 Dec 2021 13:39:13: #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 13:39:13: #2 You may need to consider one of the other alternative d(s): 2,152,173,185,553 WARNING @ Sat, 11 Dec 2021 13:39:13: #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 13:39:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:39:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:39:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:39:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.10_summits.bed INFO @ Sat, 11 Dec 2021 13:39:24: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:39:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008835/SRX9008835.20_summits.bed INFO @ Sat, 11 Dec 2021 13:39:52: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling