Job ID = 14171972 SRX = SRX7889133 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23087408 spots for SRR11283123/SRR11283123.sra Written 23087408 spots for SRR11283123/SRR11283123.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172607 ("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: 00:56:07 23087408 reads; of these: 23087408 (100.00%) were paired; of these: 6447165 (27.93%) aligned concordantly 0 times 13168184 (57.04%) aligned concordantly exactly 1 time 3472059 (15.04%) aligned concordantly >1 times ---- 6447165 pairs aligned concordantly 0 times; of these: 1176915 (18.25%) aligned discordantly 1 time ---- 5270250 pairs aligned 0 times concordantly or discordantly; of these: 10540500 mates make up the pairs; of these: 8631660 (81.89%) aligned 0 times 1123438 (10.66%) aligned exactly 1 time 785402 (7.45%) aligned >1 times 81.31% overall alignment rate Time searching: 00:56:07 Overall time: 00:56:07 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 28 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] 2674264 / 16449791 = 0.1626 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 14:55:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.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 14:55:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:07: 1000000 INFO @ Sat, 11 Dec 2021 14:55:13: 2000000 INFO @ Sat, 11 Dec 2021 14:55:21: 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 @ Sat, 11 Dec 2021 14:55:28: 4000000 INFO @ Sat, 11 Dec 2021 14:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.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 14:55:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:36: 5000000 INFO @ Sat, 11 Dec 2021 14:55:37: 1000000 INFO @ Sat, 11 Dec 2021 14:55:45: 2000000 INFO @ Sat, 11 Dec 2021 14:55:45: 6000000 INFO @ Sat, 11 Dec 2021 14:55:52: 3000000 INFO @ Sat, 11 Dec 2021 14:55:53: 7000000 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 14:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.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 14:56:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:56:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:56:01: 4000000 INFO @ Sat, 11 Dec 2021 14:56:02: 8000000 INFO @ Sat, 11 Dec 2021 14:56:08: 1000000 INFO @ Sat, 11 Dec 2021 14:56:09: 5000000 INFO @ Sat, 11 Dec 2021 14:56:10: 9000000 INFO @ Sat, 11 Dec 2021 14:56:17: 6000000 INFO @ Sat, 11 Dec 2021 14:56:17: 2000000 INFO @ Sat, 11 Dec 2021 14:56:18: 10000000 INFO @ Sat, 11 Dec 2021 14:56:26: 7000000 INFO @ Sat, 11 Dec 2021 14:56:26: 3000000 INFO @ Sat, 11 Dec 2021 14:56:27: 11000000 INFO @ Sat, 11 Dec 2021 14:56:33: 4000000 INFO @ Sat, 11 Dec 2021 14:56:34: 8000000 INFO @ Sat, 11 Dec 2021 14:56:36: 12000000 INFO @ Sat, 11 Dec 2021 14:56:40: 5000000 INFO @ Sat, 11 Dec 2021 14:56:43: 9000000 INFO @ Sat, 11 Dec 2021 14:56:44: 13000000 INFO @ Sat, 11 Dec 2021 14:56:48: 6000000 INFO @ Sat, 11 Dec 2021 14:56:51: 10000000 INFO @ Sat, 11 Dec 2021 14:56:53: 14000000 INFO @ Sat, 11 Dec 2021 14:56:55: 7000000 INFO @ Sat, 11 Dec 2021 14:56:59: 11000000 INFO @ Sat, 11 Dec 2021 14:57:01: 15000000 INFO @ Sat, 11 Dec 2021 14:57:02: 8000000 INFO @ Sat, 11 Dec 2021 14:57:08: 12000000 INFO @ Sat, 11 Dec 2021 14:57:09: 9000000 INFO @ Sat, 11 Dec 2021 14:57:10: 16000000 INFO @ Sat, 11 Dec 2021 14:57:16: 13000000 INFO @ Sat, 11 Dec 2021 14:57:17: 10000000 INFO @ Sat, 11 Dec 2021 14:57:18: 17000000 INFO @ Sat, 11 Dec 2021 14:57:24: 11000000 INFO @ Sat, 11 Dec 2021 14:57:25: 14000000 INFO @ Sat, 11 Dec 2021 14:57:27: 18000000 INFO @ Sat, 11 Dec 2021 14:57:32: 12000000 INFO @ Sat, 11 Dec 2021 14:57:33: 15000000 INFO @ Sat, 11 Dec 2021 14:57:36: 19000000 INFO @ Sat, 11 Dec 2021 14:57:40: 13000000 INFO @ Sat, 11 Dec 2021 14:57:42: 16000000 INFO @ Sat, 11 Dec 2021 14:57:44: 20000000 INFO @ Sat, 11 Dec 2021 14:57:47: 14000000 INFO @ Sat, 11 Dec 2021 14:57:50: 17000000 INFO @ Sat, 11 Dec 2021 14:57:53: 21000000 INFO @ Sat, 11 Dec 2021 14:57:54: 15000000 INFO @ Sat, 11 Dec 2021 14:57:59: 18000000 INFO @ Sat, 11 Dec 2021 14:58:01: 16000000 INFO @ Sat, 11 Dec 2021 14:58:01: 22000000 INFO @ Sat, 11 Dec 2021 14:58:07: 19000000 INFO @ Sat, 11 Dec 2021 14:58:08: 17000000 INFO @ Sat, 11 Dec 2021 14:58:10: 23000000 INFO @ Sat, 11 Dec 2021 14:58:15: 20000000 INFO @ Sat, 11 Dec 2021 14:58:16: 18000000 INFO @ Sat, 11 Dec 2021 14:58:19: 24000000 INFO @ Sat, 11 Dec 2021 14:58:23: 19000000 INFO @ Sat, 11 Dec 2021 14:58:24: 21000000 INFO @ Sat, 11 Dec 2021 14:58:28: 25000000 INFO @ Sat, 11 Dec 2021 14:58:30: 20000000 INFO @ Sat, 11 Dec 2021 14:58:32: 22000000 INFO @ Sat, 11 Dec 2021 14:58:36: 26000000 INFO @ Sat, 11 Dec 2021 14:58:37: 21000000 INFO @ Sat, 11 Dec 2021 14:58:41: 23000000 INFO @ Sat, 11 Dec 2021 14:58:45: 22000000 INFO @ Sat, 11 Dec 2021 14:58:45: 27000000 INFO @ Sat, 11 Dec 2021 14:58:50: 24000000 INFO @ Sat, 11 Dec 2021 14:58:52: 23000000 INFO @ Sat, 11 Dec 2021 14:58:54: 28000000 INFO @ Sat, 11 Dec 2021 14:58:58: 25000000 INFO @ Sat, 11 Dec 2021 14:58:59: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:59:02: 29000000 INFO @ Sat, 11 Dec 2021 14:59:06: 25000000 INFO @ Sat, 11 Dec 2021 14:59:07: 26000000 INFO @ Sat, 11 Dec 2021 14:59:11: 30000000 INFO @ Sat, 11 Dec 2021 14:59:14: 26000000 INFO @ Sat, 11 Dec 2021 14:59:16: 27000000 INFO @ Sat, 11 Dec 2021 14:59:20: 31000000 INFO @ Sat, 11 Dec 2021 14:59:21: 27000000 INFO @ Sat, 11 Dec 2021 14:59:24: 28000000 INFO @ Sat, 11 Dec 2021 14:59:28: 28000000 INFO @ Sat, 11 Dec 2021 14:59:29: 32000000 INFO @ Sat, 11 Dec 2021 14:59:31: #1 tag size is determined as 126 bps INFO @ Sat, 11 Dec 2021 14:59:31: #1 tag size = 126 INFO @ Sat, 11 Dec 2021 14:59:31: #1 total tags in treatment: 14096259 INFO @ Sat, 11 Dec 2021 14:59:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:59:31: #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 14:59:31: #1 tags after filtering in treatment: 13392816 INFO @ Sat, 11 Dec 2021 14:59:31: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 14:59:31: #1 finished! INFO @ Sat, 11 Dec 2021 14:59:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:59:32: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 14:59:32: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 14:59:32: start model_add_line... INFO @ Sat, 11 Dec 2021 14:59:32: start X-correlation... INFO @ Sat, 11 Dec 2021 14:59:32: end of X-cor INFO @ Sat, 11 Dec 2021 14:59:32: #2 finished! INFO @ Sat, 11 Dec 2021 14:59:32: #2 predicted fragment length is 239 bps INFO @ Sat, 11 Dec 2021 14:59:32: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 11 Dec 2021 14:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05_model.r WARNING @ Sat, 11 Dec 2021 14:59:32: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:59:32: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 11 Dec 2021 14:59:32: #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 14:59:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:59:33: 29000000 INFO @ Sat, 11 Dec 2021 14:59:36: 29000000 INFO @ Sat, 11 Dec 2021 14:59:41: 30000000 INFO @ Sat, 11 Dec 2021 14:59:43: 30000000 INFO @ Sat, 11 Dec 2021 14:59:50: 31000000 INFO @ Sat, 11 Dec 2021 14:59:51: 31000000 INFO @ Sat, 11 Dec 2021 14:59:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:59:58: 32000000 INFO @ Sat, 11 Dec 2021 14:59:59: 32000000 INFO @ Sat, 11 Dec 2021 15:00:00: #1 tag size is determined as 126 bps INFO @ Sat, 11 Dec 2021 15:00:00: #1 tag size = 126 INFO @ Sat, 11 Dec 2021 15:00:00: #1 total tags in treatment: 14096259 INFO @ Sat, 11 Dec 2021 15:00:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:00: #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 15:00:00: #1 tags after filtering in treatment: 13392816 INFO @ Sat, 11 Dec 2021 15:00:00: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:00:00: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:00: #1 tag size is determined as 126 bps INFO @ Sat, 11 Dec 2021 15:00:00: #1 tag size = 126 INFO @ Sat, 11 Dec 2021 15:00:00: #1 total tags in treatment: 14096259 INFO @ Sat, 11 Dec 2021 15:00:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:00:00: #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 15:00:01: #1 tags after filtering in treatment: 13392816 INFO @ Sat, 11 Dec 2021 15:00:01: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 15:00:01: #1 finished! INFO @ Sat, 11 Dec 2021 15:00:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:00:01: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 15:00:01: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:01: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:01: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:01: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:01: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:01: #2 predicted fragment length is 239 bps INFO @ Sat, 11 Dec 2021 15:00:01: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 11 Dec 2021 15:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10_model.r WARNING @ Sat, 11 Dec 2021 15:00:01: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:00:01: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 11 Dec 2021 15:00:01: #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 15:00:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:00:02: #2 number of paired peaks: 207 WARNING @ Sat, 11 Dec 2021 15:00:02: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 11 Dec 2021 15:00:02: start model_add_line... INFO @ Sat, 11 Dec 2021 15:00:02: start X-correlation... INFO @ Sat, 11 Dec 2021 15:00:02: end of X-cor INFO @ Sat, 11 Dec 2021 15:00:02: #2 finished! INFO @ Sat, 11 Dec 2021 15:00:02: #2 predicted fragment length is 239 bps INFO @ Sat, 11 Dec 2021 15:00:02: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 11 Dec 2021 15:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20_model.r WARNING @ Sat, 11 Dec 2021 15:00:02: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:00:02: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 11 Dec 2021 15:00:02: #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 15:00:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:00:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.05_summits.bed INFO @ Sat, 11 Dec 2021 15:00:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3669 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:00:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.10_summits.bed INFO @ Sat, 11 Dec 2021 15:00:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1846 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:00:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889133/SRX7889133.20_summits.bed INFO @ Sat, 11 Dec 2021 15:00:41: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (816 records, 4 fields): 3 millis CompletedMACS2peakCalling