Job ID = 14172045 SRX = SRX9103808 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25895080 spots for SRR12621008/SRR12621008.sra Written 25895080 spots for SRR12621008/SRR12621008.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172586 ("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: 00:33:58 25895080 reads; of these: 25895080 (100.00%) were paired; of these: 9470402 (36.57%) aligned concordantly 0 times 9123841 (35.23%) aligned concordantly exactly 1 time 7300837 (28.19%) aligned concordantly >1 times ---- 9470402 pairs aligned concordantly 0 times; of these: 1331039 (14.05%) aligned discordantly 1 time ---- 8139363 pairs aligned 0 times concordantly or discordantly; of these: 16278726 mates make up the pairs; of these: 14653039 (90.01%) aligned 0 times 505310 (3.10%) aligned exactly 1 time 1120377 (6.88%) aligned >1 times 71.71% overall alignment rate Time searching: 00:33:58 Overall time: 00:33:58 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] 4947039 / 17597989 = 0.2811 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 14:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.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 14:39:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:39:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:39:42: 1000000 INFO @ Sat, 11 Dec 2021 14:39:48: 2000000 INFO @ Sat, 11 Dec 2021 14:39:55: 3000000 INFO @ Sat, 11 Dec 2021 14:40:01: 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 14:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.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 14:40:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:40:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:40:07: 5000000 INFO @ Sat, 11 Dec 2021 14:40:14: 1000000 INFO @ Sat, 11 Dec 2021 14:40:14: 6000000 INFO @ Sat, 11 Dec 2021 14:40:20: 7000000 INFO @ Sat, 11 Dec 2021 14:40:21: 2000000 INFO @ Sat, 11 Dec 2021 14:40:27: 8000000 INFO @ Sat, 11 Dec 2021 14:40:29: 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 @ Sat, 11 Dec 2021 14:40:34: 9000000 INFO @ Sat, 11 Dec 2021 14:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.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 14:40:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:40:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:40:37: 4000000 INFO @ Sat, 11 Dec 2021 14:40:40: 10000000 INFO @ Sat, 11 Dec 2021 14:40:43: 1000000 INFO @ Sat, 11 Dec 2021 14:40:45: 5000000 INFO @ Sat, 11 Dec 2021 14:40:47: 11000000 INFO @ Sat, 11 Dec 2021 14:40:50: 2000000 INFO @ Sat, 11 Dec 2021 14:40:53: 6000000 INFO @ Sat, 11 Dec 2021 14:40:54: 12000000 INFO @ Sat, 11 Dec 2021 14:40:57: 3000000 INFO @ Sat, 11 Dec 2021 14:41:00: 7000000 INFO @ Sat, 11 Dec 2021 14:41:01: 13000000 INFO @ Sat, 11 Dec 2021 14:41:04: 4000000 INFO @ Sat, 11 Dec 2021 14:41:08: 8000000 INFO @ Sat, 11 Dec 2021 14:41:08: 14000000 INFO @ Sat, 11 Dec 2021 14:41:11: 5000000 INFO @ Sat, 11 Dec 2021 14:41:15: 15000000 INFO @ Sat, 11 Dec 2021 14:41:16: 9000000 INFO @ Sat, 11 Dec 2021 14:41:17: 6000000 INFO @ Sat, 11 Dec 2021 14:41:22: 16000000 INFO @ Sat, 11 Dec 2021 14:41:24: 10000000 INFO @ Sat, 11 Dec 2021 14:41:24: 7000000 INFO @ Sat, 11 Dec 2021 14:41:28: 17000000 INFO @ Sat, 11 Dec 2021 14:41:31: 8000000 INFO @ Sat, 11 Dec 2021 14:41:32: 11000000 INFO @ Sat, 11 Dec 2021 14:41:35: 18000000 INFO @ Sat, 11 Dec 2021 14:41:38: 9000000 INFO @ Sat, 11 Dec 2021 14:41:40: 12000000 INFO @ Sat, 11 Dec 2021 14:41:42: 19000000 INFO @ Sat, 11 Dec 2021 14:41:45: 10000000 INFO @ Sat, 11 Dec 2021 14:41:48: 13000000 INFO @ Sat, 11 Dec 2021 14:41:48: 20000000 INFO @ Sat, 11 Dec 2021 14:41:52: 11000000 INFO @ Sat, 11 Dec 2021 14:41:54: 21000000 INFO @ Sat, 11 Dec 2021 14:41:55: 14000000 INFO @ Sat, 11 Dec 2021 14:41:59: 12000000 INFO @ Sat, 11 Dec 2021 14:42:02: 22000000 INFO @ Sat, 11 Dec 2021 14:42:03: 15000000 INFO @ Sat, 11 Dec 2021 14:42:06: 13000000 INFO @ Sat, 11 Dec 2021 14:42:09: 23000000 INFO @ Sat, 11 Dec 2021 14:42:11: 16000000 INFO @ Sat, 11 Dec 2021 14:42:13: 14000000 INFO @ Sat, 11 Dec 2021 14:42:16: 24000000 INFO @ Sat, 11 Dec 2021 14:42:19: 17000000 INFO @ Sat, 11 Dec 2021 14:42:20: 15000000 INFO @ Sat, 11 Dec 2021 14:42:23: 25000000 INFO @ Sat, 11 Dec 2021 14:42:27: 16000000 INFO @ Sat, 11 Dec 2021 14:42:27: 18000000 INFO @ Sat, 11 Dec 2021 14:42:30: 26000000 INFO @ Sat, 11 Dec 2021 14:42:34: 17000000 INFO @ Sat, 11 Dec 2021 14:42:35: 19000000 INFO @ Sat, 11 Dec 2021 14:42:37: 27000000 INFO @ Sat, 11 Dec 2021 14:42:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:42:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:42:38: #1 total tags in treatment: 11566317 INFO @ Sat, 11 Dec 2021 14:42:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:42:38: #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 14:42:39: #1 tags after filtering in treatment: 8954806 INFO @ Sat, 11 Dec 2021 14:42:39: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:42:39: #1 finished! INFO @ Sat, 11 Dec 2021 14:42:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:42:39: #2 number of paired peaks: 783 WARNING @ Sat, 11 Dec 2021 14:42:39: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Sat, 11 Dec 2021 14:42:39: start model_add_line... INFO @ Sat, 11 Dec 2021 14:42:40: start X-correlation... INFO @ Sat, 11 Dec 2021 14:42:40: end of X-cor INFO @ Sat, 11 Dec 2021 14:42:40: #2 finished! INFO @ Sat, 11 Dec 2021 14:42:40: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:42:40: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05_model.r WARNING @ Sat, 11 Dec 2021 14:42:40: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:42:40: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:42:40: #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 14:42:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:42:41: 18000000 INFO @ Sat, 11 Dec 2021 14:42:43: 20000000 INFO @ Sat, 11 Dec 2021 14:42:47: 19000000 INFO @ Sat, 11 Dec 2021 14:42:50: 21000000 INFO @ Sat, 11 Dec 2021 14:42:54: 20000000 INFO @ Sat, 11 Dec 2021 14:42:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:42:58: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:43:00: 21000000 INFO @ Sat, 11 Dec 2021 14:43:06: 23000000 INFO @ Sat, 11 Dec 2021 14:43:07: 22000000 INFO @ Sat, 11 Dec 2021 14:43:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:43:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:43:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.05_summits.bed INFO @ Sat, 11 Dec 2021 14:43:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8415 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:43:14: 24000000 INFO @ Sat, 11 Dec 2021 14:43:14: 23000000 INFO @ Sat, 11 Dec 2021 14:43:20: 24000000 INFO @ Sat, 11 Dec 2021 14:43:21: 25000000 INFO @ Sat, 11 Dec 2021 14:43:26: 25000000 INFO @ Sat, 11 Dec 2021 14:43:29: 26000000 INFO @ Sat, 11 Dec 2021 14:43:33: 26000000 INFO @ Sat, 11 Dec 2021 14:43:37: 27000000 INFO @ Sat, 11 Dec 2021 14:43:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:43:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:43:39: #1 total tags in treatment: 11566317 INFO @ Sat, 11 Dec 2021 14:43:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:43:39: #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 14:43:39: 27000000 INFO @ Sat, 11 Dec 2021 14:43:40: #1 tags after filtering in treatment: 8954806 INFO @ Sat, 11 Dec 2021 14:43:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:43:40: #1 finished! INFO @ Sat, 11 Dec 2021 14:43:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:43:40: #2 number of paired peaks: 783 WARNING @ Sat, 11 Dec 2021 14:43:40: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Sat, 11 Dec 2021 14:43:40: start model_add_line... INFO @ Sat, 11 Dec 2021 14:43:40: start X-correlation... INFO @ Sat, 11 Dec 2021 14:43:40: end of X-cor INFO @ Sat, 11 Dec 2021 14:43:40: #2 finished! INFO @ Sat, 11 Dec 2021 14:43:40: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:43:40: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10_model.r WARNING @ Sat, 11 Dec 2021 14:43:40: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:43:40: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:43:40: #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 14:43:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:43:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:43:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:43:41: #1 total tags in treatment: 11566317 INFO @ Sat, 11 Dec 2021 14:43:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:43:41: #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 14:43:41: #1 tags after filtering in treatment: 8954806 INFO @ Sat, 11 Dec 2021 14:43:41: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 14:43:41: #1 finished! INFO @ Sat, 11 Dec 2021 14:43:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:43:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:43:42: #2 number of paired peaks: 783 WARNING @ Sat, 11 Dec 2021 14:43:42: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Sat, 11 Dec 2021 14:43:42: start model_add_line... INFO @ Sat, 11 Dec 2021 14:43:42: start X-correlation... INFO @ Sat, 11 Dec 2021 14:43:42: end of X-cor INFO @ Sat, 11 Dec 2021 14:43:42: #2 finished! INFO @ Sat, 11 Dec 2021 14:43:42: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 14:43:42: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 14:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20_model.r WARNING @ Sat, 11 Dec 2021 14:43:42: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:43:42: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 14:43:42: #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 14:43:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:43:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:43:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:44:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.10_summits.bed INFO @ Sat, 11 Dec 2021 14:44:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4248 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103808/SRX9103808.20_summits.bed INFO @ Sat, 11 Dec 2021 14:44:10: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1034 records, 4 fields): 4 millis CompletedMACS2peakCalling