Job ID = 12265645 SRX = SRX7277049 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31252483 spots for SRR10597314/SRR10597314.sra Written 31252483 spots for SRR10597314/SRR10597314.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266183 ("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: 00:48:25 31252483 reads; of these: 31252483 (100.00%) were paired; of these: 1646607 (5.27%) aligned concordantly 0 times 13104002 (41.93%) aligned concordantly exactly 1 time 16501874 (52.80%) aligned concordantly >1 times ---- 1646607 pairs aligned concordantly 0 times; of these: 479213 (29.10%) aligned discordantly 1 time ---- 1167394 pairs aligned 0 times concordantly or discordantly; of these: 2334788 mates make up the pairs; of these: 1126609 (48.25%) aligned 0 times 451925 (19.36%) aligned exactly 1 time 756254 (32.39%) aligned >1 times 98.20% overall alignment rate Time searching: 00:48:25 Overall time: 00:48:25 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] 12238324 / 29990442 = 0.4081 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.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, 03 Apr 2021 08:59:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:59:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:59:18: 1000000 INFO @ Sat, 03 Apr 2021 08:59:23: 2000000 INFO @ Sat, 03 Apr 2021 08:59:28: 3000000 INFO @ Sat, 03 Apr 2021 08:59:34: 4000000 INFO @ Sat, 03 Apr 2021 08:59:39: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.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, 03 Apr 2021 08:59:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:59:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:59:44: 6000000 INFO @ Sat, 03 Apr 2021 08:59:47: 1000000 INFO @ Sat, 03 Apr 2021 08:59:50: 7000000 INFO @ Sat, 03 Apr 2021 08:59:52: 2000000 INFO @ Sat, 03 Apr 2021 08:59:55: 8000000 INFO @ Sat, 03 Apr 2021 08:59:57: 3000000 INFO @ Sat, 03 Apr 2021 09:00:00: 9000000 INFO @ Sat, 03 Apr 2021 09:00:03: 4000000 INFO @ Sat, 03 Apr 2021 09:00:06: 10000000 INFO @ Sat, 03 Apr 2021 09:00:08: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:00:11: 11000000 INFO @ Sat, 03 Apr 2021 09:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.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, 03 Apr 2021 09:00:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:00:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:00:14: 6000000 INFO @ Sat, 03 Apr 2021 09:00:16: 12000000 INFO @ Sat, 03 Apr 2021 09:00:18: 1000000 INFO @ Sat, 03 Apr 2021 09:00:20: 7000000 INFO @ Sat, 03 Apr 2021 09:00:22: 13000000 INFO @ Sat, 03 Apr 2021 09:00:24: 2000000 INFO @ Sat, 03 Apr 2021 09:00:26: 8000000 INFO @ Sat, 03 Apr 2021 09:00:27: 14000000 INFO @ Sat, 03 Apr 2021 09:00:30: 3000000 INFO @ Sat, 03 Apr 2021 09:00:32: 9000000 INFO @ Sat, 03 Apr 2021 09:00:33: 15000000 INFO @ Sat, 03 Apr 2021 09:00:35: 4000000 INFO @ Sat, 03 Apr 2021 09:00:38: 10000000 INFO @ Sat, 03 Apr 2021 09:00:38: 16000000 INFO @ Sat, 03 Apr 2021 09:00:41: 5000000 INFO @ Sat, 03 Apr 2021 09:00:44: 17000000 INFO @ Sat, 03 Apr 2021 09:00:44: 11000000 INFO @ Sat, 03 Apr 2021 09:00:47: 6000000 INFO @ Sat, 03 Apr 2021 09:00:49: 18000000 INFO @ Sat, 03 Apr 2021 09:00:50: 12000000 INFO @ Sat, 03 Apr 2021 09:00:53: 7000000 INFO @ Sat, 03 Apr 2021 09:00:55: 19000000 INFO @ Sat, 03 Apr 2021 09:00:56: 13000000 INFO @ Sat, 03 Apr 2021 09:01:00: 8000000 INFO @ Sat, 03 Apr 2021 09:01:00: 20000000 INFO @ Sat, 03 Apr 2021 09:01:01: 14000000 INFO @ Sat, 03 Apr 2021 09:01:05: 9000000 INFO @ Sat, 03 Apr 2021 09:01:06: 21000000 INFO @ Sat, 03 Apr 2021 09:01:07: 15000000 INFO @ Sat, 03 Apr 2021 09:01:11: 22000000 INFO @ Sat, 03 Apr 2021 09:01:11: 10000000 INFO @ Sat, 03 Apr 2021 09:01:13: 16000000 INFO @ Sat, 03 Apr 2021 09:01:16: 23000000 INFO @ Sat, 03 Apr 2021 09:01:17: 11000000 INFO @ Sat, 03 Apr 2021 09:01:19: 17000000 INFO @ Sat, 03 Apr 2021 09:01:22: 24000000 INFO @ Sat, 03 Apr 2021 09:01:23: 12000000 INFO @ Sat, 03 Apr 2021 09:01:25: 18000000 INFO @ Sat, 03 Apr 2021 09:01:27: 25000000 INFO @ Sat, 03 Apr 2021 09:01:29: 13000000 INFO @ Sat, 03 Apr 2021 09:01:31: 19000000 INFO @ Sat, 03 Apr 2021 09:01:32: 26000000 INFO @ Sat, 03 Apr 2021 09:01:35: 14000000 INFO @ Sat, 03 Apr 2021 09:01:36: 20000000 INFO @ Sat, 03 Apr 2021 09:01:38: 27000000 INFO @ Sat, 03 Apr 2021 09:01:41: 15000000 INFO @ Sat, 03 Apr 2021 09:01:42: 21000000 INFO @ Sat, 03 Apr 2021 09:01:43: 28000000 INFO @ Sat, 03 Apr 2021 09:01:48: 16000000 INFO @ Sat, 03 Apr 2021 09:01:48: 29000000 INFO @ Sat, 03 Apr 2021 09:01:48: 22000000 INFO @ Sat, 03 Apr 2021 09:01:53: 17000000 INFO @ Sat, 03 Apr 2021 09:01:54: 30000000 INFO @ Sat, 03 Apr 2021 09:01:54: 23000000 INFO @ Sat, 03 Apr 2021 09:01:59: 31000000 INFO @ Sat, 03 Apr 2021 09:01:59: 18000000 INFO @ Sat, 03 Apr 2021 09:02:00: 24000000 INFO @ Sat, 03 Apr 2021 09:02:05: 19000000 INFO @ Sat, 03 Apr 2021 09:02:05: 32000000 INFO @ Sat, 03 Apr 2021 09:02:05: 25000000 INFO @ Sat, 03 Apr 2021 09:02:11: 20000000 INFO @ Sat, 03 Apr 2021 09:02:11: 33000000 INFO @ Sat, 03 Apr 2021 09:02:11: 26000000 INFO @ Sat, 03 Apr 2021 09:02:16: 34000000 INFO @ Sat, 03 Apr 2021 09:02:16: 21000000 INFO @ Sat, 03 Apr 2021 09:02:17: 27000000 INFO @ Sat, 03 Apr 2021 09:02:22: 35000000 INFO @ Sat, 03 Apr 2021 09:02:23: 22000000 INFO @ Sat, 03 Apr 2021 09:02:23: 28000000 INFO @ Sat, 03 Apr 2021 09:02:29: 36000000 INFO @ Sat, 03 Apr 2021 09:02:30: 29000000 INFO @ Sat, 03 Apr 2021 09:02:30: 23000000 INFO @ Sat, 03 Apr 2021 09:02:35: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:02:35: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:02:35: #1 total tags in treatment: 17402471 INFO @ Sat, 03 Apr 2021 09:02:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:02:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:02:35: #1 tags after filtering in treatment: 13261192 INFO @ Sat, 03 Apr 2021 09:02:35: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 09:02:35: #1 finished! INFO @ Sat, 03 Apr 2021 09:02:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:02:36: #2 number of paired peaks: 129 WARNING @ Sat, 03 Apr 2021 09:02:36: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 03 Apr 2021 09:02:36: start model_add_line... INFO @ Sat, 03 Apr 2021 09:02:36: start X-correlation... INFO @ Sat, 03 Apr 2021 09:02:36: end of X-cor INFO @ Sat, 03 Apr 2021 09:02:36: #2 finished! INFO @ Sat, 03 Apr 2021 09:02:36: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 09:02:36: #2 alternative fragment length(s) may be 3,52,120,597 bps INFO @ Sat, 03 Apr 2021 09:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05_model.r WARNING @ Sat, 03 Apr 2021 09:02:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:02:36: #2 You may need to consider one of the other alternative d(s): 3,52,120,597 WARNING @ Sat, 03 Apr 2021 09:02:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:02:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:02:36: 30000000 INFO @ Sat, 03 Apr 2021 09:02:37: 24000000 INFO @ Sat, 03 Apr 2021 09:02:43: 31000000 INFO @ Sat, 03 Apr 2021 09:02:44: 25000000 INFO @ Sat, 03 Apr 2021 09:02:50: 32000000 INFO @ Sat, 03 Apr 2021 09:02:50: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:02:57: 33000000 INFO @ Sat, 03 Apr 2021 09:02:57: 27000000 INFO @ Sat, 03 Apr 2021 09:02:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:03:04: 28000000 INFO @ Sat, 03 Apr 2021 09:03:04: 34000000 INFO @ Sat, 03 Apr 2021 09:03:11: 29000000 INFO @ Sat, 03 Apr 2021 09:03:11: 35000000 INFO @ Sat, 03 Apr 2021 09:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.05_summits.bed INFO @ Sat, 03 Apr 2021 09:03:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3635 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:03:18: 30000000 INFO @ Sat, 03 Apr 2021 09:03:18: 36000000 INFO @ Sat, 03 Apr 2021 09:03:24: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:03:24: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:03:24: #1 total tags in treatment: 17402471 INFO @ Sat, 03 Apr 2021 09:03:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:03:25: 31000000 INFO @ Sat, 03 Apr 2021 09:03:25: #1 tags after filtering in treatment: 13261192 INFO @ Sat, 03 Apr 2021 09:03:25: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 09:03:25: #1 finished! INFO @ Sat, 03 Apr 2021 09:03:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:03:26: #2 number of paired peaks: 129 WARNING @ Sat, 03 Apr 2021 09:03:26: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 03 Apr 2021 09:03:26: start model_add_line... INFO @ Sat, 03 Apr 2021 09:03:26: start X-correlation... INFO @ Sat, 03 Apr 2021 09:03:26: end of X-cor INFO @ Sat, 03 Apr 2021 09:03:26: #2 finished! INFO @ Sat, 03 Apr 2021 09:03:26: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 09:03:26: #2 alternative fragment length(s) may be 3,52,120,597 bps INFO @ Sat, 03 Apr 2021 09:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10_model.r WARNING @ Sat, 03 Apr 2021 09:03:26: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:03:26: #2 You may need to consider one of the other alternative d(s): 3,52,120,597 WARNING @ Sat, 03 Apr 2021 09:03:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:03:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:03:31: 32000000 INFO @ Sat, 03 Apr 2021 09:03:37: 33000000 INFO @ Sat, 03 Apr 2021 09:03:43: 34000000 INFO @ Sat, 03 Apr 2021 09:03:50: 35000000 INFO @ Sat, 03 Apr 2021 09:03:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:03:56: 36000000 INFO @ Sat, 03 Apr 2021 09:04:02: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:04:02: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:04:02: #1 total tags in treatment: 17402471 INFO @ Sat, 03 Apr 2021 09:04:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:04:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:04:02: #1 tags after filtering in treatment: 13261192 INFO @ Sat, 03 Apr 2021 09:04:02: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 09:04:02: #1 finished! INFO @ Sat, 03 Apr 2021 09:04:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:04:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:04:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:04:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.10_summits.bed INFO @ Sat, 03 Apr 2021 09:04:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:04:03: #2 number of paired peaks: 129 WARNING @ Sat, 03 Apr 2021 09:04:03: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 03 Apr 2021 09:04:03: start model_add_line... INFO @ Sat, 03 Apr 2021 09:04:03: start X-correlation... INFO @ Sat, 03 Apr 2021 09:04:03: end of X-cor INFO @ Sat, 03 Apr 2021 09:04:03: #2 finished! INFO @ Sat, 03 Apr 2021 09:04:03: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 09:04:03: #2 alternative fragment length(s) may be 3,52,120,597 bps INFO @ Sat, 03 Apr 2021 09:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20_model.r WARNING @ Sat, 03 Apr 2021 09:04:03: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:04:03: #2 You may need to consider one of the other alternative d(s): 3,52,120,597 WARNING @ Sat, 03 Apr 2021 09:04:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:04:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:04:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:04:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277049/SRX7277049.20_summits.bed INFO @ Sat, 03 Apr 2021 09:04:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (288 records, 4 fields): 2 millis CompletedMACS2peakCalling