Job ID = 14168676 SRX = ERX3978879 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34169973 spots for ERR3975948/ERR3975948.sra Written 34169973 spots for ERR3975948/ERR3975948.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169958 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:42:02 34169973 reads; of these: 34169973 (100.00%) were paired; of these: 5403154 (15.81%) aligned concordantly 0 times 21926366 (64.17%) aligned concordantly exactly 1 time 6840453 (20.02%) aligned concordantly >1 times ---- 5403154 pairs aligned concordantly 0 times; of these: 773179 (14.31%) aligned discordantly 1 time ---- 4629975 pairs aligned 0 times concordantly or discordantly; of these: 9259950 mates make up the pairs; of these: 3998989 (43.19%) aligned 0 times 2458185 (26.55%) aligned exactly 1 time 2802776 (30.27%) aligned >1 times 94.15% overall alignment rate Time searching: 02:42:03 Overall time: 02:42:03 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] 19703025 / 29204130 = 0.6747 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 @ Fri, 10 Dec 2021 22:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.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 @ Fri, 10 Dec 2021 22:23:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:23:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:23:19: 1000000 INFO @ Fri, 10 Dec 2021 22:23:29: 2000000 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 @ Fri, 10 Dec 2021 22:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.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 @ Fri, 10 Dec 2021 22:23:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:23:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:23:39: 3000000 INFO @ Fri, 10 Dec 2021 22:23:47: 1000000 INFO @ Fri, 10 Dec 2021 22:23:48: 4000000 INFO @ Fri, 10 Dec 2021 22:23:55: 2000000 INFO @ Fri, 10 Dec 2021 22:23:58: 5000000 INFO @ Fri, 10 Dec 2021 22:24:04: 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 @ Fri, 10 Dec 2021 22:24:07: 6000000 INFO @ Fri, 10 Dec 2021 22:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.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 @ Fri, 10 Dec 2021 22:24:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:24:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:24:12: 4000000 INFO @ Fri, 10 Dec 2021 22:24:17: 7000000 INFO @ Fri, 10 Dec 2021 22:24:17: 1000000 INFO @ Fri, 10 Dec 2021 22:24:20: 5000000 INFO @ Fri, 10 Dec 2021 22:24:26: 8000000 INFO @ Fri, 10 Dec 2021 22:24:26: 2000000 INFO @ Fri, 10 Dec 2021 22:24:28: 6000000 INFO @ Fri, 10 Dec 2021 22:24:35: 3000000 INFO @ Fri, 10 Dec 2021 22:24:35: 9000000 INFO @ Fri, 10 Dec 2021 22:24:36: 7000000 INFO @ Fri, 10 Dec 2021 22:24:43: 4000000 INFO @ Fri, 10 Dec 2021 22:24:45: 8000000 INFO @ Fri, 10 Dec 2021 22:24:45: 10000000 INFO @ Fri, 10 Dec 2021 22:24:51: 5000000 INFO @ Fri, 10 Dec 2021 22:24:53: 9000000 INFO @ Fri, 10 Dec 2021 22:24:54: 11000000 INFO @ Fri, 10 Dec 2021 22:25:00: 6000000 INFO @ Fri, 10 Dec 2021 22:25:02: 10000000 INFO @ Fri, 10 Dec 2021 22:25:03: 12000000 INFO @ Fri, 10 Dec 2021 22:25:07: 7000000 INFO @ Fri, 10 Dec 2021 22:25:10: 11000000 INFO @ Fri, 10 Dec 2021 22:25:13: 13000000 INFO @ Fri, 10 Dec 2021 22:25:15: 8000000 INFO @ Fri, 10 Dec 2021 22:25:18: 12000000 INFO @ Fri, 10 Dec 2021 22:25:22: 14000000 INFO @ Fri, 10 Dec 2021 22:25:23: 9000000 INFO @ Fri, 10 Dec 2021 22:25:26: 13000000 INFO @ Fri, 10 Dec 2021 22:25:31: 10000000 INFO @ Fri, 10 Dec 2021 22:25:32: 15000000 INFO @ Fri, 10 Dec 2021 22:25:34: 14000000 INFO @ Fri, 10 Dec 2021 22:25:39: 11000000 INFO @ Fri, 10 Dec 2021 22:25:41: 16000000 INFO @ Fri, 10 Dec 2021 22:25:43: 15000000 INFO @ Fri, 10 Dec 2021 22:25:47: 12000000 INFO @ Fri, 10 Dec 2021 22:25:50: 17000000 INFO @ Fri, 10 Dec 2021 22:25:51: 16000000 INFO @ Fri, 10 Dec 2021 22:25:55: 13000000 INFO @ Fri, 10 Dec 2021 22:25:59: 17000000 INFO @ Fri, 10 Dec 2021 22:25:59: 18000000 INFO @ Fri, 10 Dec 2021 22:26:03: 14000000 INFO @ Fri, 10 Dec 2021 22:26:07: 18000000 INFO @ Fri, 10 Dec 2021 22:26:08: 19000000 INFO @ Fri, 10 Dec 2021 22:26:11: 15000000 INFO @ Fri, 10 Dec 2021 22:26:15: 19000000 INFO @ Fri, 10 Dec 2021 22:26:18: 20000000 INFO @ Fri, 10 Dec 2021 22:26:19: 16000000 INFO @ Fri, 10 Dec 2021 22:26:23: 20000000 INFO @ Fri, 10 Dec 2021 22:26:27: 21000000 INFO @ Fri, 10 Dec 2021 22:26:27: 17000000 INFO @ Fri, 10 Dec 2021 22:26:32: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:26:36: 18000000 INFO @ Fri, 10 Dec 2021 22:26:36: 22000000 INFO @ Fri, 10 Dec 2021 22:26:40: 22000000 INFO @ Fri, 10 Dec 2021 22:26:44: 19000000 INFO @ Fri, 10 Dec 2021 22:26:46: 23000000 INFO @ Fri, 10 Dec 2021 22:26:48: 23000000 INFO @ Fri, 10 Dec 2021 22:26:52: 20000000 INFO @ Fri, 10 Dec 2021 22:26:55: 24000000 INFO @ Fri, 10 Dec 2021 22:26:57: 24000000 INFO @ Fri, 10 Dec 2021 22:27:01: 21000000 INFO @ Fri, 10 Dec 2021 22:27:03: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 22:27:03: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 22:27:03: #1 total tags in treatment: 9432157 INFO @ Fri, 10 Dec 2021 22:27:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:27:04: #1 tags after filtering in treatment: 8553691 INFO @ Fri, 10 Dec 2021 22:27:04: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 22:27:04: #1 finished! INFO @ Fri, 10 Dec 2021 22:27:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:27:05: #2 number of paired peaks: 1915 INFO @ Fri, 10 Dec 2021 22:27:05: start model_add_line... INFO @ Fri, 10 Dec 2021 22:27:05: start X-correlation... INFO @ Fri, 10 Dec 2021 22:27:05: end of X-cor INFO @ Fri, 10 Dec 2021 22:27:05: #2 finished! INFO @ Fri, 10 Dec 2021 22:27:05: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 22:27:05: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 22:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05_model.r WARNING @ Fri, 10 Dec 2021 22:27:05: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:27:05: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 22:27:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:27:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:27:05: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 22:27:05: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 22:27:05: #1 total tags in treatment: 9432157 INFO @ Fri, 10 Dec 2021 22:27:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:27:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:27:05: #1 tags after filtering in treatment: 8553691 INFO @ Fri, 10 Dec 2021 22:27:05: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 22:27:05: #1 finished! INFO @ Fri, 10 Dec 2021 22:27:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:27:06: #2 number of paired peaks: 1915 INFO @ Fri, 10 Dec 2021 22:27:06: start model_add_line... INFO @ Fri, 10 Dec 2021 22:27:06: start X-correlation... INFO @ Fri, 10 Dec 2021 22:27:06: end of X-cor INFO @ Fri, 10 Dec 2021 22:27:06: #2 finished! INFO @ Fri, 10 Dec 2021 22:27:06: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 22:27:06: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 22:27:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10_model.r WARNING @ Fri, 10 Dec 2021 22:27:06: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:27:06: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 22:27:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:27:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:27:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:27:09: 22000000 INFO @ Fri, 10 Dec 2021 22:27:17: 23000000 INFO @ Fri, 10 Dec 2021 22:27:24: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:27:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:27:31: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 22:27:31: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 22:27:31: #1 total tags in treatment: 9432157 INFO @ Fri, 10 Dec 2021 22:27:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:27:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:27:31: #1 tags after filtering in treatment: 8553691 INFO @ Fri, 10 Dec 2021 22:27:31: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 22:27:31: #1 finished! INFO @ Fri, 10 Dec 2021 22:27:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:27:32: #2 number of paired peaks: 1915 INFO @ Fri, 10 Dec 2021 22:27:32: start model_add_line... INFO @ Fri, 10 Dec 2021 22:27:32: start X-correlation... INFO @ Fri, 10 Dec 2021 22:27:32: end of X-cor INFO @ Fri, 10 Dec 2021 22:27:32: #2 finished! INFO @ Fri, 10 Dec 2021 22:27:32: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 22:27:32: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 22:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20_model.r WARNING @ Fri, 10 Dec 2021 22:27:32: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:27:32: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 22:27:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:27:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:27:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.05_summits.bed INFO @ Fri, 10 Dec 2021 22:27:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11037 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.10_summits.bed INFO @ Fri, 10 Dec 2021 22:27:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7025 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:27:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978879/ERX3978879.20_summits.bed INFO @ Fri, 10 Dec 2021 22:28:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3931 records, 4 fields): 7 millis CompletedMACS2peakCalling