Job ID = 16437562 SRX = ERX5847870 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:43:05 prefetch.2.10.7: 1) Downloading 'ERR6212880'... 2022-08-02T03:43:05 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:43:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:43:52 prefetch.2.10.7: 'ERR6212880' is valid 2022-08-02T03:43:52 prefetch.2.10.7: 1) 'ERR6212880' was downloaded successfully 2022-08-02T03:43:52 prefetch.2.10.7: 'ERR6212880' has 0 unresolved dependencies Read 10612400 spots for ERR6212880/ERR6212880.sra Written 10612400 spots for ERR6212880/ERR6212880.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437606 ("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: 00:05:41 10612400 reads; of these: 10612400 (100.00%) were paired; of these: 3131287 (29.51%) aligned concordantly 0 times 6923746 (65.24%) aligned concordantly exactly 1 time 557367 (5.25%) aligned concordantly >1 times ---- 3131287 pairs aligned concordantly 0 times; of these: 19210 (0.61%) aligned discordantly 1 time ---- 3112077 pairs aligned 0 times concordantly or discordantly; of these: 6224154 mates make up the pairs; of these: 5191042 (83.40%) aligned 0 times 936670 (15.05%) aligned exactly 1 time 96442 (1.55%) aligned >1 times 75.54% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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 8 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] 129301 / 7498133 = 0.0172 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 12:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.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 12:56:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:56:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:56:15: 1000000 INFO @ Tue, 02 Aug 2022 12:56:20: 2000000 INFO @ Tue, 02 Aug 2022 12:56:25: 3000000 INFO @ Tue, 02 Aug 2022 12:56:30: 4000000 INFO @ Tue, 02 Aug 2022 12:56:35: 5000000 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 12:56:39: 6000000 INFO @ Tue, 02 Aug 2022 12:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.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 12:56:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:56:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:56:45: 7000000 INFO @ Tue, 02 Aug 2022 12:56:45: 1000000 INFO @ Tue, 02 Aug 2022 12:56:50: 8000000 INFO @ Tue, 02 Aug 2022 12:56:51: 2000000 INFO @ Tue, 02 Aug 2022 12:56:55: 9000000 INFO @ Tue, 02 Aug 2022 12:56:56: 3000000 INFO @ Tue, 02 Aug 2022 12:57:00: 10000000 INFO @ Tue, 02 Aug 2022 12:57:01: 4000000 INFO @ Tue, 02 Aug 2022 12:57:05: 11000000 INFO @ Tue, 02 Aug 2022 12:57:06: 5000000 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 12:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.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 12:57:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:57:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:57:11: 12000000 INFO @ Tue, 02 Aug 2022 12:57:12: 6000000 INFO @ Tue, 02 Aug 2022 12:57:15: 1000000 INFO @ Tue, 02 Aug 2022 12:57:16: 13000000 INFO @ Tue, 02 Aug 2022 12:57:17: 7000000 INFO @ Tue, 02 Aug 2022 12:57:21: 2000000 INFO @ Tue, 02 Aug 2022 12:57:21: 14000000 INFO @ Tue, 02 Aug 2022 12:57:22: 8000000 INFO @ Tue, 02 Aug 2022 12:57:26: 3000000 INFO @ Tue, 02 Aug 2022 12:57:27: 15000000 INFO @ Tue, 02 Aug 2022 12:57:28: 9000000 INFO @ Tue, 02 Aug 2022 12:57:31: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:57:31: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:57:31: #1 total tags in treatment: 7351848 INFO @ Tue, 02 Aug 2022 12:57:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:57:31: #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 12:57:31: #1 tags after filtering in treatment: 6824727 INFO @ Tue, 02 Aug 2022 12:57:31: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 12:57:31: #1 finished! INFO @ Tue, 02 Aug 2022 12:57:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:57:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:57:32: 4000000 INFO @ Tue, 02 Aug 2022 12:57:32: #2 number of paired peaks: 10456 INFO @ Tue, 02 Aug 2022 12:57:32: start model_add_line... INFO @ Tue, 02 Aug 2022 12:57:32: start X-correlation... INFO @ Tue, 02 Aug 2022 12:57:32: end of X-cor INFO @ Tue, 02 Aug 2022 12:57:32: #2 finished! INFO @ Tue, 02 Aug 2022 12:57:32: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 12:57:32: #2 alternative fragment length(s) may be 3,175 bps INFO @ Tue, 02 Aug 2022 12:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05_model.r INFO @ Tue, 02 Aug 2022 12:57:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:57:33: 10000000 INFO @ Tue, 02 Aug 2022 12:57:37: 5000000 INFO @ Tue, 02 Aug 2022 12:57:39: 11000000 INFO @ Tue, 02 Aug 2022 12:57:42: 6000000 INFO @ Tue, 02 Aug 2022 12:57:44: 12000000 INFO @ Tue, 02 Aug 2022 12:57:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:57:48: 7000000 INFO @ Tue, 02 Aug 2022 12:57:49: 13000000 INFO @ Tue, 02 Aug 2022 12:57:53: 8000000 INFO @ Tue, 02 Aug 2022 12:57:55: 14000000 INFO @ Tue, 02 Aug 2022 12:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.05_summits.bed INFO @ Tue, 02 Aug 2022 12:57:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6625 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:57:59: 9000000 INFO @ Tue, 02 Aug 2022 12:58:00: 15000000 INFO @ Tue, 02 Aug 2022 12:58:04: 10000000 INFO @ Tue, 02 Aug 2022 12:58:04: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:58:04: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:58:04: #1 total tags in treatment: 7351848 INFO @ Tue, 02 Aug 2022 12:58:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:58:04: #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 12:58:04: #1 tags after filtering in treatment: 6824727 INFO @ Tue, 02 Aug 2022 12:58:04: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 12:58:04: #1 finished! INFO @ Tue, 02 Aug 2022 12:58:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:58:05: #2 number of paired peaks: 10456 INFO @ Tue, 02 Aug 2022 12:58:05: start model_add_line... INFO @ Tue, 02 Aug 2022 12:58:05: start X-correlation... INFO @ Tue, 02 Aug 2022 12:58:05: end of X-cor INFO @ Tue, 02 Aug 2022 12:58:05: #2 finished! INFO @ Tue, 02 Aug 2022 12:58:05: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 12:58:05: #2 alternative fragment length(s) may be 3,175 bps INFO @ Tue, 02 Aug 2022 12:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10_model.r INFO @ Tue, 02 Aug 2022 12:58:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:58:09: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:58:14: 12000000 INFO @ Tue, 02 Aug 2022 12:58:19: 13000000 INFO @ Tue, 02 Aug 2022 12:58:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:58:24: 14000000 INFO @ Tue, 02 Aug 2022 12:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:58:29: 15000000 INFO @ Tue, 02 Aug 2022 12:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.10_summits.bed INFO @ Tue, 02 Aug 2022 12:58:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3744 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:58:33: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:58:33: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:58:33: #1 total tags in treatment: 7351848 INFO @ Tue, 02 Aug 2022 12:58:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:58:33: #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 12:58:33: #1 tags after filtering in treatment: 6824727 INFO @ Tue, 02 Aug 2022 12:58:33: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 12:58:33: #1 finished! INFO @ Tue, 02 Aug 2022 12:58:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:58:34: #2 number of paired peaks: 10456 INFO @ Tue, 02 Aug 2022 12:58:34: start model_add_line... INFO @ Tue, 02 Aug 2022 12:58:34: start X-correlation... INFO @ Tue, 02 Aug 2022 12:58:34: end of X-cor INFO @ Tue, 02 Aug 2022 12:58:34: #2 finished! INFO @ Tue, 02 Aug 2022 12:58:34: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 12:58:34: #2 alternative fragment length(s) may be 3,175 bps INFO @ Tue, 02 Aug 2022 12:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20_model.r INFO @ Tue, 02 Aug 2022 12:58:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:58:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:58:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847870/ERX5847870.20_summits.bed INFO @ Tue, 02 Aug 2022 12:58:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1174 records, 4 fields): 23 millis CompletedMACS2peakCalling