Job ID = 16437420 SRX = ERX9180699 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:25:00 prefetch.2.10.7: 1) Downloading 'ERR9627607'... 2022-08-02T03:25:00 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:27:40 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:27:40 prefetch.2.10.7: 1) 'ERR9627607' was downloaded successfully 2022-08-02T03:27:40 prefetch.2.10.7: 'ERR9627607' has 0 unresolved dependencies Read 58342521 spots for ERR9627607/ERR9627607.sra Written 58342521 spots for ERR9627607/ERR9627607.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438522 ("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: 01:17:02 58342521 reads; of these: 58342521 (100.00%) were paired; of these: 37277015 (63.89%) aligned concordantly 0 times 15009472 (25.73%) aligned concordantly exactly 1 time 6056034 (10.38%) aligned concordantly >1 times ---- 37277015 pairs aligned concordantly 0 times; of these: 4521333 (12.13%) aligned discordantly 1 time ---- 32755682 pairs aligned 0 times concordantly or discordantly; of these: 65511364 mates make up the pairs; of these: 57244341 (87.38%) aligned 0 times 3710566 (5.66%) aligned exactly 1 time 4556457 (6.96%) aligned >1 times 50.94% overall alignment rate Time searching: 01:17:02 Overall time: 01:17:02 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 24 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] 10666654 / 25509794 = 0.4181 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 14:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.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 14:09:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:42: 1000000 INFO @ Tue, 02 Aug 2022 14:09:50: 2000000 INFO @ Tue, 02 Aug 2022 14:09:59: 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 14:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.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 14:10:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:07: 4000000 INFO @ Tue, 02 Aug 2022 14:10:13: 1000000 INFO @ Tue, 02 Aug 2022 14:10:15: 5000000 INFO @ Tue, 02 Aug 2022 14:10:21: 2000000 INFO @ Tue, 02 Aug 2022 14:10:23: 6000000 INFO @ Tue, 02 Aug 2022 14:10:29: 3000000 INFO @ Tue, 02 Aug 2022 14:10:31: 7000000 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 14:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.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 14:10:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:10:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:10:37: 4000000 INFO @ Tue, 02 Aug 2022 14:10:39: 8000000 INFO @ Tue, 02 Aug 2022 14:10:42: 1000000 INFO @ Tue, 02 Aug 2022 14:10:45: 5000000 INFO @ Tue, 02 Aug 2022 14:10:47: 9000000 INFO @ Tue, 02 Aug 2022 14:10:51: 2000000 INFO @ Tue, 02 Aug 2022 14:10:53: 6000000 INFO @ Tue, 02 Aug 2022 14:10:56: 10000000 INFO @ Tue, 02 Aug 2022 14:10:59: 3000000 INFO @ Tue, 02 Aug 2022 14:11:01: 7000000 INFO @ Tue, 02 Aug 2022 14:11:04: 11000000 INFO @ Tue, 02 Aug 2022 14:11:07: 4000000 INFO @ Tue, 02 Aug 2022 14:11:10: 8000000 INFO @ Tue, 02 Aug 2022 14:11:12: 12000000 INFO @ Tue, 02 Aug 2022 14:11:15: 5000000 INFO @ Tue, 02 Aug 2022 14:11:18: 9000000 INFO @ Tue, 02 Aug 2022 14:11:20: 13000000 INFO @ Tue, 02 Aug 2022 14:11:23: 6000000 INFO @ Tue, 02 Aug 2022 14:11:26: 10000000 INFO @ Tue, 02 Aug 2022 14:11:29: 14000000 INFO @ Tue, 02 Aug 2022 14:11:31: 7000000 INFO @ Tue, 02 Aug 2022 14:11:34: 11000000 INFO @ Tue, 02 Aug 2022 14:11:37: 15000000 INFO @ Tue, 02 Aug 2022 14:11:39: 8000000 INFO @ Tue, 02 Aug 2022 14:11:42: 12000000 INFO @ Tue, 02 Aug 2022 14:11:44: 16000000 INFO @ Tue, 02 Aug 2022 14:11:47: 9000000 INFO @ Tue, 02 Aug 2022 14:11:50: 13000000 INFO @ Tue, 02 Aug 2022 14:11:52: 17000000 INFO @ Tue, 02 Aug 2022 14:11:55: 10000000 INFO @ Tue, 02 Aug 2022 14:11:58: 14000000 INFO @ Tue, 02 Aug 2022 14:12:00: 18000000 INFO @ Tue, 02 Aug 2022 14:12:03: 11000000 INFO @ Tue, 02 Aug 2022 14:12:06: 15000000 INFO @ Tue, 02 Aug 2022 14:12:08: 19000000 INFO @ Tue, 02 Aug 2022 14:12:10: 12000000 INFO @ Tue, 02 Aug 2022 14:12:13: 16000000 INFO @ Tue, 02 Aug 2022 14:12:15: 20000000 INFO @ Tue, 02 Aug 2022 14:12:18: 13000000 INFO @ Tue, 02 Aug 2022 14:12:21: 17000000 INFO @ Tue, 02 Aug 2022 14:12:22: 21000000 INFO @ Tue, 02 Aug 2022 14:12:25: 14000000 INFO @ Tue, 02 Aug 2022 14:12:29: 18000000 INFO @ Tue, 02 Aug 2022 14:12:29: 22000000 INFO @ Tue, 02 Aug 2022 14:12:33: 15000000 INFO @ Tue, 02 Aug 2022 14:12:37: 23000000 INFO @ Tue, 02 Aug 2022 14:12:37: 19000000 INFO @ Tue, 02 Aug 2022 14:12:41: 16000000 INFO @ Tue, 02 Aug 2022 14:12:43: 24000000 INFO @ Tue, 02 Aug 2022 14:12:45: 20000000 INFO @ Tue, 02 Aug 2022 14:12:48: 17000000 INFO @ Tue, 02 Aug 2022 14:12:49: 25000000 INFO @ Tue, 02 Aug 2022 14:12:53: 21000000 INFO @ Tue, 02 Aug 2022 14:12:55: 26000000 INFO @ Tue, 02 Aug 2022 14:12:55: 18000000 INFO @ Tue, 02 Aug 2022 14:13:00: 22000000 INFO @ Tue, 02 Aug 2022 14:13:01: 27000000 INFO @ Tue, 02 Aug 2022 14:13:03: 19000000 INFO @ Tue, 02 Aug 2022 14:13:07: 28000000 INFO @ Tue, 02 Aug 2022 14:13:08: 23000000 INFO @ Tue, 02 Aug 2022 14:13:10: 20000000 INFO @ Tue, 02 Aug 2022 14:13:14: 29000000 INFO @ Tue, 02 Aug 2022 14:13:15: 24000000 INFO @ Tue, 02 Aug 2022 14:13:18: 21000000 INFO @ Tue, 02 Aug 2022 14:13:20: 30000000 INFO @ Tue, 02 Aug 2022 14:13:23: 25000000 INFO @ Tue, 02 Aug 2022 14:13:25: 22000000 INFO @ Tue, 02 Aug 2022 14:13:27: 31000000 INFO @ Tue, 02 Aug 2022 14:13:31: 26000000 INFO @ Tue, 02 Aug 2022 14:13:32: 23000000 INFO @ Tue, 02 Aug 2022 14:13:33: 32000000 INFO @ Tue, 02 Aug 2022 14:13:39: 27000000 INFO @ Tue, 02 Aug 2022 14:13:39: 24000000 INFO @ Tue, 02 Aug 2022 14:13:40: 33000000 INFO @ Tue, 02 Aug 2022 14:13:46: 28000000 INFO @ Tue, 02 Aug 2022 14:13:47: 25000000 INFO @ Tue, 02 Aug 2022 14:13:47: 34000000 INFO @ Tue, 02 Aug 2022 14:13:54: 29000000 INFO @ Tue, 02 Aug 2022 14:13:54: 35000000 INFO @ Tue, 02 Aug 2022 14:13:55: 26000000 INFO @ Tue, 02 Aug 2022 14:14:01: 36000000 INFO @ Tue, 02 Aug 2022 14:14:02: 30000000 INFO @ Tue, 02 Aug 2022 14:14:03: 27000000 INFO @ Tue, 02 Aug 2022 14:14:08: 37000000 INFO @ Tue, 02 Aug 2022 14:14:10: 31000000 INFO @ Tue, 02 Aug 2022 14:14:11: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:14:15: 38000000 INFO @ Tue, 02 Aug 2022 14:14:16: #1 tag size is determined as 45 bps INFO @ Tue, 02 Aug 2022 14:14:16: #1 tag size = 45 INFO @ Tue, 02 Aug 2022 14:14:16: #1 total tags in treatment: 12029389 INFO @ Tue, 02 Aug 2022 14:14:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:16: #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 14:14:16: #1 tags after filtering in treatment: 11257742 INFO @ Tue, 02 Aug 2022 14:14:16: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 14:14:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:17: #2 number of paired peaks: 871 WARNING @ Tue, 02 Aug 2022 14:14:17: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 02 Aug 2022 14:14:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:17: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:14:17: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05_model.r INFO @ Tue, 02 Aug 2022 14:14:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:18: 32000000 INFO @ Tue, 02 Aug 2022 14:14:18: 29000000 INFO @ Tue, 02 Aug 2022 14:14:27: 33000000 INFO @ Tue, 02 Aug 2022 14:14:27: 30000000 INFO @ Tue, 02 Aug 2022 14:14:35: 34000000 INFO @ Tue, 02 Aug 2022 14:14:35: 31000000 INFO @ Tue, 02 Aug 2022 14:14:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:43: 35000000 INFO @ Tue, 02 Aug 2022 14:14:43: 32000000 INFO @ Tue, 02 Aug 2022 14:14:51: 36000000 INFO @ Tue, 02 Aug 2022 14:14:51: 33000000 INFO @ Tue, 02 Aug 2022 14:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.05_summits.bed INFO @ Tue, 02 Aug 2022 14:14:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3023 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:59: 37000000 INFO @ Tue, 02 Aug 2022 14:15:00: 34000000 INFO @ Tue, 02 Aug 2022 14:15:08: 38000000 INFO @ Tue, 02 Aug 2022 14:15:08: 35000000 INFO @ Tue, 02 Aug 2022 14:15:08: #1 tag size is determined as 45 bps INFO @ Tue, 02 Aug 2022 14:15:08: #1 tag size = 45 INFO @ Tue, 02 Aug 2022 14:15:08: #1 total tags in treatment: 12029389 INFO @ Tue, 02 Aug 2022 14:15:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:15:08: #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 14:15:09: #1 tags after filtering in treatment: 11257742 INFO @ Tue, 02 Aug 2022 14:15:09: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 14:15:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:15:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:15:09: #2 number of paired peaks: 871 WARNING @ Tue, 02 Aug 2022 14:15:09: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 02 Aug 2022 14:15:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:15:10: start X-correlation... INFO @ Tue, 02 Aug 2022 14:15:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:15:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:15:10: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:15:10: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10_model.r INFO @ Tue, 02 Aug 2022 14:15:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:15:16: 36000000 INFO @ Tue, 02 Aug 2022 14:15:24: 37000000 INFO @ Tue, 02 Aug 2022 14:15:31: 38000000 INFO @ Tue, 02 Aug 2022 14:15:32: #1 tag size is determined as 45 bps INFO @ Tue, 02 Aug 2022 14:15:32: #1 tag size = 45 INFO @ Tue, 02 Aug 2022 14:15:32: #1 total tags in treatment: 12029389 INFO @ Tue, 02 Aug 2022 14:15:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:15:32: #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 14:15:32: #1 tags after filtering in treatment: 11257742 INFO @ Tue, 02 Aug 2022 14:15:32: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 14:15:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:15:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:15:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:15:33: #2 number of paired peaks: 871 WARNING @ Tue, 02 Aug 2022 14:15:33: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 02 Aug 2022 14:15:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:15:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:15:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:15:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:15:33: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:15:33: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:15:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20_model.r INFO @ Tue, 02 Aug 2022 14:15:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:15:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.10_summits.bed INFO @ Tue, 02 Aug 2022 14:15:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1598 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:15:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9180699/ERX9180699.20_summits.bed INFO @ Tue, 02 Aug 2022 14:16:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 21 millis CompletedMACS2peakCalling