Job ID = 14172154 SRX = SRX9786715 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15028074 spots for SRR13362634/SRR13362634.sra Written 15028074 spots for SRR13362634/SRR13362634.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172655 ("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: 00:14:28 15028074 reads; of these: 15028074 (100.00%) were paired; of these: 3615757 (24.06%) aligned concordantly 0 times 6694264 (44.55%) aligned concordantly exactly 1 time 4718053 (31.39%) aligned concordantly >1 times ---- 3615757 pairs aligned concordantly 0 times; of these: 927106 (25.64%) aligned discordantly 1 time ---- 2688651 pairs aligned 0 times concordantly or discordantly; of these: 5377302 mates make up the pairs; of these: 4063940 (75.58%) aligned 0 times 437680 (8.14%) aligned exactly 1 time 875682 (16.28%) aligned >1 times 86.48% overall alignment rate Time searching: 00:14:28 Overall time: 00:14:28 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 12 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] 3700139 / 12225874 = 0.3026 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 14:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.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 14:52:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:12: 1000000 INFO @ Sat, 11 Dec 2021 14:52:17: 2000000 INFO @ Sat, 11 Dec 2021 14:52:23: 3000000 INFO @ Sat, 11 Dec 2021 14:52:28: 4000000 INFO @ Sat, 11 Dec 2021 14:52:33: 5000000 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 14:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.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 14:52:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:39: 6000000 INFO @ Sat, 11 Dec 2021 14:52:44: 1000000 INFO @ Sat, 11 Dec 2021 14:52:46: 7000000 INFO @ Sat, 11 Dec 2021 14:52:52: 2000000 INFO @ Sat, 11 Dec 2021 14:52:53: 8000000 INFO @ Sat, 11 Dec 2021 14:53:00: 3000000 INFO @ Sat, 11 Dec 2021 14:53:00: 9000000 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 14:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.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 14:53:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:53:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:53:07: 10000000 INFO @ Sat, 11 Dec 2021 14:53:08: 4000000 INFO @ Sat, 11 Dec 2021 14:53:14: 11000000 INFO @ Sat, 11 Dec 2021 14:53:15: 1000000 INFO @ Sat, 11 Dec 2021 14:53:16: 5000000 INFO @ Sat, 11 Dec 2021 14:53:21: 12000000 INFO @ Sat, 11 Dec 2021 14:53:23: 2000000 INFO @ Sat, 11 Dec 2021 14:53:24: 6000000 INFO @ Sat, 11 Dec 2021 14:53:28: 13000000 INFO @ Sat, 11 Dec 2021 14:53:31: 3000000 INFO @ Sat, 11 Dec 2021 14:53:32: 7000000 INFO @ Sat, 11 Dec 2021 14:53:35: 14000000 INFO @ Sat, 11 Dec 2021 14:53:39: 4000000 INFO @ Sat, 11 Dec 2021 14:53:40: 8000000 INFO @ Sat, 11 Dec 2021 14:53:42: 15000000 INFO @ Sat, 11 Dec 2021 14:53:47: 5000000 INFO @ Sat, 11 Dec 2021 14:53:48: 9000000 INFO @ Sat, 11 Dec 2021 14:53:50: 16000000 INFO @ Sat, 11 Dec 2021 14:53:55: 6000000 INFO @ Sat, 11 Dec 2021 14:53:56: 10000000 INFO @ Sat, 11 Dec 2021 14:53:57: 17000000 INFO @ Sat, 11 Dec 2021 14:54:03: 7000000 INFO @ Sat, 11 Dec 2021 14:54:04: 18000000 INFO @ Sat, 11 Dec 2021 14:54:04: 11000000 INFO @ Sat, 11 Dec 2021 14:54:08: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:54:08: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:54:08: #1 total tags in treatment: 7801059 INFO @ Sat, 11 Dec 2021 14:54:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:54:08: #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 14:54:08: #1 tags after filtering in treatment: 6185917 INFO @ Sat, 11 Dec 2021 14:54:08: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:54:08: #1 finished! INFO @ Sat, 11 Dec 2021 14:54:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:54:08: #2 number of paired peaks: 1510 INFO @ Sat, 11 Dec 2021 14:54:08: start model_add_line... INFO @ Sat, 11 Dec 2021 14:54:08: start X-correlation... INFO @ Sat, 11 Dec 2021 14:54:08: end of X-cor INFO @ Sat, 11 Dec 2021 14:54:08: #2 finished! INFO @ Sat, 11 Dec 2021 14:54:08: #2 predicted fragment length is 83 bps INFO @ Sat, 11 Dec 2021 14:54:08: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 11 Dec 2021 14:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05_model.r WARNING @ Sat, 11 Dec 2021 14:54:08: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:54:08: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 11 Dec 2021 14:54:08: #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 14:54:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:54:11: 8000000 INFO @ Sat, 11 Dec 2021 14:54:12: 12000000 INFO @ Sat, 11 Dec 2021 14:54:19: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:54:19: 13000000 INFO @ Sat, 11 Dec 2021 14:54:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:54:27: 10000000 INFO @ Sat, 11 Dec 2021 14:54:27: 14000000 INFO @ Sat, 11 Dec 2021 14:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.05_summits.bed INFO @ Sat, 11 Dec 2021 14:54:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7553 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:54:35: 11000000 INFO @ Sat, 11 Dec 2021 14:54:35: 15000000 INFO @ Sat, 11 Dec 2021 14:54:43: 12000000 INFO @ Sat, 11 Dec 2021 14:54:43: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:54:51: 13000000 INFO @ Sat, 11 Dec 2021 14:54:51: 17000000 INFO @ Sat, 11 Dec 2021 14:54:58: 14000000 INFO @ Sat, 11 Dec 2021 14:54:59: 18000000 INFO @ Sat, 11 Dec 2021 14:55:03: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:55:03: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:55:03: #1 total tags in treatment: 7801059 INFO @ Sat, 11 Dec 2021 14:55:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:55:03: #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 14:55:03: #1 tags after filtering in treatment: 6185917 INFO @ Sat, 11 Dec 2021 14:55:03: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:55:03: #1 finished! INFO @ Sat, 11 Dec 2021 14:55:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:55:04: #2 number of paired peaks: 1510 INFO @ Sat, 11 Dec 2021 14:55:04: start model_add_line... INFO @ Sat, 11 Dec 2021 14:55:04: start X-correlation... INFO @ Sat, 11 Dec 2021 14:55:04: end of X-cor INFO @ Sat, 11 Dec 2021 14:55:04: #2 finished! INFO @ Sat, 11 Dec 2021 14:55:04: #2 predicted fragment length is 83 bps INFO @ Sat, 11 Dec 2021 14:55:04: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 11 Dec 2021 14:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10_model.r WARNING @ Sat, 11 Dec 2021 14:55:04: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:55:04: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 11 Dec 2021 14:55:04: #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 14:55:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:55:06: 15000000 INFO @ Sat, 11 Dec 2021 14:55:13: 16000000 INFO @ Sat, 11 Dec 2021 14:55:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:55:20: 17000000 INFO @ Sat, 11 Dec 2021 14:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.10_summits.bed INFO @ Sat, 11 Dec 2021 14:55:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3637 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:55:27: 18000000 INFO @ Sat, 11 Dec 2021 14:55:31: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:55:31: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:55:31: #1 total tags in treatment: 7801059 INFO @ Sat, 11 Dec 2021 14:55:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:55:31: #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 14:55:31: #1 tags after filtering in treatment: 6185917 INFO @ Sat, 11 Dec 2021 14:55:31: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:55:31: #1 finished! INFO @ Sat, 11 Dec 2021 14:55:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:55:32: #2 number of paired peaks: 1510 INFO @ Sat, 11 Dec 2021 14:55:32: start model_add_line... INFO @ Sat, 11 Dec 2021 14:55:32: start X-correlation... INFO @ Sat, 11 Dec 2021 14:55:32: end of X-cor INFO @ Sat, 11 Dec 2021 14:55:32: #2 finished! INFO @ Sat, 11 Dec 2021 14:55:32: #2 predicted fragment length is 83 bps INFO @ Sat, 11 Dec 2021 14:55:32: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 11 Dec 2021 14:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20_model.r WARNING @ Sat, 11 Dec 2021 14:55:32: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:55:32: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 11 Dec 2021 14:55:32: #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 14:55:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:55:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786715/SRX9786715.20_summits.bed INFO @ Sat, 11 Dec 2021 14:55:51: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 2 millis CompletedMACS2peakCalling