Job ID = 16440065 SRX = SRX10855779 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18546111 spots for SRR14509966/SRR14509966.sra Written 18546111 spots for SRR14509966/SRR14509966.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440717 ("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: 00:51:01 18546111 reads; of these: 18546111 (100.00%) were paired; of these: 1790456 (9.65%) aligned concordantly 0 times 12390743 (66.81%) aligned concordantly exactly 1 time 4364912 (23.54%) aligned concordantly >1 times ---- 1790456 pairs aligned concordantly 0 times; of these: 337278 (18.84%) aligned discordantly 1 time ---- 1453178 pairs aligned 0 times concordantly or discordantly; of these: 2906356 mates make up the pairs; of these: 1852216 (63.73%) aligned 0 times 727459 (25.03%) aligned exactly 1 time 326681 (11.24%) aligned >1 times 95.01% overall alignment rate Time searching: 00:51:01 Overall time: 00:51:01 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] 1952985 / 17041868 = 0.1146 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.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 @ Tue, 02 Aug 2022 17:56:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:56:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:56:46: 1000000 INFO @ Tue, 02 Aug 2022 17:56:55: 2000000 INFO @ Tue, 02 Aug 2022 17:57:04: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.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 @ Tue, 02 Aug 2022 17:57:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:57:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:57:13: 4000000 INFO @ Tue, 02 Aug 2022 17:57:16: 1000000 INFO @ Tue, 02 Aug 2022 17:57:23: 5000000 INFO @ Tue, 02 Aug 2022 17:57:26: 2000000 INFO @ Tue, 02 Aug 2022 17:57:32: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:57:35: 3000000 INFO @ Tue, 02 Aug 2022 17:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.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 @ Tue, 02 Aug 2022 17:57:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:57:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:57:42: 7000000 INFO @ Tue, 02 Aug 2022 17:57:45: 4000000 INFO @ Tue, 02 Aug 2022 17:57:46: 1000000 INFO @ Tue, 02 Aug 2022 17:57:52: 8000000 INFO @ Tue, 02 Aug 2022 17:57:55: 5000000 INFO @ Tue, 02 Aug 2022 17:57:57: 2000000 INFO @ Tue, 02 Aug 2022 17:58:02: 9000000 INFO @ Tue, 02 Aug 2022 17:58:04: 6000000 INFO @ Tue, 02 Aug 2022 17:58:06: 3000000 INFO @ Tue, 02 Aug 2022 17:58:12: 10000000 INFO @ Tue, 02 Aug 2022 17:58:14: 7000000 INFO @ Tue, 02 Aug 2022 17:58:16: 4000000 INFO @ Tue, 02 Aug 2022 17:58:21: 11000000 INFO @ Tue, 02 Aug 2022 17:58:23: 8000000 INFO @ Tue, 02 Aug 2022 17:58:26: 5000000 INFO @ Tue, 02 Aug 2022 17:58:31: 12000000 INFO @ Tue, 02 Aug 2022 17:58:32: 9000000 INFO @ Tue, 02 Aug 2022 17:58:35: 6000000 INFO @ Tue, 02 Aug 2022 17:58:41: 13000000 INFO @ Tue, 02 Aug 2022 17:58:42: 10000000 INFO @ Tue, 02 Aug 2022 17:58:45: 7000000 INFO @ Tue, 02 Aug 2022 17:58:50: 14000000 INFO @ Tue, 02 Aug 2022 17:58:51: 11000000 INFO @ Tue, 02 Aug 2022 17:58:54: 8000000 INFO @ Tue, 02 Aug 2022 17:59:00: 15000000 INFO @ Tue, 02 Aug 2022 17:59:01: 12000000 INFO @ Tue, 02 Aug 2022 17:59:04: 9000000 INFO @ Tue, 02 Aug 2022 17:59:10: 16000000 INFO @ Tue, 02 Aug 2022 17:59:10: 13000000 INFO @ Tue, 02 Aug 2022 17:59:13: 10000000 INFO @ Tue, 02 Aug 2022 17:59:19: 14000000 INFO @ Tue, 02 Aug 2022 17:59:20: 17000000 INFO @ Tue, 02 Aug 2022 17:59:23: 11000000 INFO @ Tue, 02 Aug 2022 17:59:29: 15000000 INFO @ Tue, 02 Aug 2022 17:59:29: 18000000 INFO @ Tue, 02 Aug 2022 17:59:32: 12000000 INFO @ Tue, 02 Aug 2022 17:59:38: 16000000 INFO @ Tue, 02 Aug 2022 17:59:40: 19000000 INFO @ Tue, 02 Aug 2022 17:59:41: 13000000 INFO @ Tue, 02 Aug 2022 17:59:48: 17000000 INFO @ Tue, 02 Aug 2022 17:59:50: 20000000 INFO @ Tue, 02 Aug 2022 17:59:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:59:58: 18000000 INFO @ Tue, 02 Aug 2022 17:59:59: 21000000 INFO @ Tue, 02 Aug 2022 18:00:01: 15000000 INFO @ Tue, 02 Aug 2022 18:00:08: 19000000 INFO @ Tue, 02 Aug 2022 18:00:09: 22000000 INFO @ Tue, 02 Aug 2022 18:00:10: 16000000 INFO @ Tue, 02 Aug 2022 18:00:18: 20000000 INFO @ Tue, 02 Aug 2022 18:00:19: 23000000 INFO @ Tue, 02 Aug 2022 18:00:21: 17000000 INFO @ Tue, 02 Aug 2022 18:00:28: 21000000 INFO @ Tue, 02 Aug 2022 18:00:29: 24000000 INFO @ Tue, 02 Aug 2022 18:00:30: 18000000 INFO @ Tue, 02 Aug 2022 18:00:38: 22000000 INFO @ Tue, 02 Aug 2022 18:00:38: 25000000 INFO @ Tue, 02 Aug 2022 18:00:40: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:00:47: 23000000 INFO @ Tue, 02 Aug 2022 18:00:48: 26000000 INFO @ Tue, 02 Aug 2022 18:00:50: 20000000 INFO @ Tue, 02 Aug 2022 18:00:57: 27000000 INFO @ Tue, 02 Aug 2022 18:00:57: 24000000 INFO @ Tue, 02 Aug 2022 18:00:59: 21000000 INFO @ Tue, 02 Aug 2022 18:01:07: 25000000 INFO @ Tue, 02 Aug 2022 18:01:07: 28000000 INFO @ Tue, 02 Aug 2022 18:01:08: 22000000 INFO @ Tue, 02 Aug 2022 18:01:16: 26000000 INFO @ Tue, 02 Aug 2022 18:01:17: 29000000 INFO @ Tue, 02 Aug 2022 18:01:17: 23000000 INFO @ Tue, 02 Aug 2022 18:01:26: 27000000 INFO @ Tue, 02 Aug 2022 18:01:26: 30000000 INFO @ Tue, 02 Aug 2022 18:01:27: 24000000 INFO @ Tue, 02 Aug 2022 18:01:36: 28000000 INFO @ Tue, 02 Aug 2022 18:01:36: 31000000 INFO @ Tue, 02 Aug 2022 18:01:37: 25000000 INFO @ Tue, 02 Aug 2022 18:01:39: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:01:39: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:01:39: #1 total tags in treatment: 14815297 INFO @ Tue, 02 Aug 2022 18:01:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:01:40: #1 tags after filtering in treatment: 11109865 INFO @ Tue, 02 Aug 2022 18:01:40: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:01:40: #1 finished! INFO @ Tue, 02 Aug 2022 18:01:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:01:41: #2 number of paired peaks: 2618 INFO @ Tue, 02 Aug 2022 18:01:41: start model_add_line... INFO @ Tue, 02 Aug 2022 18:01:41: start X-correlation... INFO @ Tue, 02 Aug 2022 18:01:41: end of X-cor INFO @ Tue, 02 Aug 2022 18:01:41: #2 finished! INFO @ Tue, 02 Aug 2022 18:01:41: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 18:01:41: #2 alternative fragment length(s) may be 1,175 bps INFO @ Tue, 02 Aug 2022 18:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05_model.r WARNING @ Tue, 02 Aug 2022 18:01:41: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:01:41: #2 You may need to consider one of the other alternative d(s): 1,175 WARNING @ Tue, 02 Aug 2022 18:01:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:01:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:01:45: 29000000 INFO @ Tue, 02 Aug 2022 18:01:46: 26000000 INFO @ Tue, 02 Aug 2022 18:01:54: 30000000 INFO @ Tue, 02 Aug 2022 18:01:55: 27000000 INFO @ Tue, 02 Aug 2022 18:02:03: 31000000 INFO @ Tue, 02 Aug 2022 18:02:04: 28000000 INFO @ Tue, 02 Aug 2022 18:02:06: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:02:06: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:02:06: #1 total tags in treatment: 14815297 INFO @ Tue, 02 Aug 2022 18:02:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:02:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:02:06: #1 tags after filtering in treatment: 11109865 INFO @ Tue, 02 Aug 2022 18:02:06: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:02:06: #1 finished! INFO @ Tue, 02 Aug 2022 18:02:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:02:07: #2 number of paired peaks: 2618 INFO @ Tue, 02 Aug 2022 18:02:07: start model_add_line... INFO @ Tue, 02 Aug 2022 18:02:08: start X-correlation... INFO @ Tue, 02 Aug 2022 18:02:08: end of X-cor INFO @ Tue, 02 Aug 2022 18:02:08: #2 finished! INFO @ Tue, 02 Aug 2022 18:02:08: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 18:02:08: #2 alternative fragment length(s) may be 1,175 bps INFO @ Tue, 02 Aug 2022 18:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10_model.r WARNING @ Tue, 02 Aug 2022 18:02:08: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:02:08: #2 You may need to consider one of the other alternative d(s): 1,175 WARNING @ Tue, 02 Aug 2022 18:02:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:02:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:02:12: 29000000 INFO @ Tue, 02 Aug 2022 18:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.05_summits.bed INFO @ Tue, 02 Aug 2022 18:02:19: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1734 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:02:21: 30000000 INFO @ Tue, 02 Aug 2022 18:02:29: 31000000 INFO @ Tue, 02 Aug 2022 18:02:31: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:02:31: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:02:31: #1 total tags in treatment: 14815297 INFO @ Tue, 02 Aug 2022 18:02:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:02:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:02:32: #1 tags after filtering in treatment: 11109865 INFO @ Tue, 02 Aug 2022 18:02:32: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 02 Aug 2022 18:02:32: #1 finished! INFO @ Tue, 02 Aug 2022 18:02:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:02:33: #2 number of paired peaks: 2618 INFO @ Tue, 02 Aug 2022 18:02:33: start model_add_line... INFO @ Tue, 02 Aug 2022 18:02:33: start X-correlation... INFO @ Tue, 02 Aug 2022 18:02:33: end of X-cor INFO @ Tue, 02 Aug 2022 18:02:33: #2 finished! INFO @ Tue, 02 Aug 2022 18:02:33: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 18:02:33: #2 alternative fragment length(s) may be 1,175 bps INFO @ Tue, 02 Aug 2022 18:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20_model.r WARNING @ Tue, 02 Aug 2022 18:02:33: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:02:33: #2 You may need to consider one of the other alternative d(s): 1,175 WARNING @ Tue, 02 Aug 2022 18:02:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:02:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:02:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.10_summits.bed INFO @ Tue, 02 Aug 2022 18:02:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (801 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:02:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855779/SRX10855779.20_summits.bed INFO @ Tue, 02 Aug 2022 18:03:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 15 millis CompletedMACS2peakCalling