Job ID = 16436225 SRX = SRX12178871 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:09:37 prefetch.2.10.7: 1) Downloading 'SRR15888043'... 2022-08-02T02:09:37 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:11:10 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:11:10 prefetch.2.10.7: 1) 'SRR15888043' was downloaded successfully 2022-08-02T02:11:10 prefetch.2.10.7: 'SRR15888043' has 0 unresolved dependencies Read 26162181 spots for SRR15888043/SRR15888043.sra Written 26162181 spots for SRR15888043/SRR15888043.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436575 ("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: 00:23:07 26162181 reads; of these: 26162181 (100.00%) were paired; of these: 8157900 (31.18%) aligned concordantly 0 times 15596259 (59.61%) aligned concordantly exactly 1 time 2408022 (9.20%) aligned concordantly >1 times ---- 8157900 pairs aligned concordantly 0 times; of these: 2935730 (35.99%) aligned discordantly 1 time ---- 5222170 pairs aligned 0 times concordantly or discordantly; of these: 10444340 mates make up the pairs; of these: 7179287 (68.74%) aligned 0 times 2379795 (22.79%) aligned exactly 1 time 885258 (8.48%) aligned >1 times 86.28% overall alignment rate Time searching: 00:23:08 Overall time: 00:23:08 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 20 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] 4324247 / 20873399 = 0.2072 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 11:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.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 11:47:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:12: 1000000 INFO @ Tue, 02 Aug 2022 11:47:18: 2000000 INFO @ Tue, 02 Aug 2022 11:47:24: 3000000 INFO @ Tue, 02 Aug 2022 11:47:29: 4000000 INFO @ Tue, 02 Aug 2022 11:47:35: 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 11:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.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 11:47:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:41: 6000000 INFO @ Tue, 02 Aug 2022 11:47:44: 1000000 INFO @ Tue, 02 Aug 2022 11:47:48: 7000000 INFO @ Tue, 02 Aug 2022 11:47:51: 2000000 INFO @ Tue, 02 Aug 2022 11:47:54: 8000000 INFO @ Tue, 02 Aug 2022 11:47:57: 3000000 INFO @ Tue, 02 Aug 2022 11:48:00: 9000000 INFO @ Tue, 02 Aug 2022 11:48:04: 4000000 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 11:48:07: 10000000 INFO @ Tue, 02 Aug 2022 11:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.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 11:48:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:10: 5000000 INFO @ Tue, 02 Aug 2022 11:48:13: 11000000 INFO @ Tue, 02 Aug 2022 11:48:14: 1000000 INFO @ Tue, 02 Aug 2022 11:48:16: 6000000 INFO @ Tue, 02 Aug 2022 11:48:19: 12000000 INFO @ Tue, 02 Aug 2022 11:48:20: 2000000 INFO @ Tue, 02 Aug 2022 11:48:22: 7000000 INFO @ Tue, 02 Aug 2022 11:48:26: 13000000 INFO @ Tue, 02 Aug 2022 11:48:26: 3000000 INFO @ Tue, 02 Aug 2022 11:48:28: 8000000 INFO @ Tue, 02 Aug 2022 11:48:32: 14000000 INFO @ Tue, 02 Aug 2022 11:48:33: 4000000 INFO @ Tue, 02 Aug 2022 11:48:34: 9000000 INFO @ Tue, 02 Aug 2022 11:48:39: 15000000 INFO @ Tue, 02 Aug 2022 11:48:39: 5000000 INFO @ Tue, 02 Aug 2022 11:48:40: 10000000 INFO @ Tue, 02 Aug 2022 11:48:45: 16000000 INFO @ Tue, 02 Aug 2022 11:48:45: 11000000 INFO @ Tue, 02 Aug 2022 11:48:46: 6000000 INFO @ Tue, 02 Aug 2022 11:48:51: 12000000 INFO @ Tue, 02 Aug 2022 11:48:51: 17000000 INFO @ Tue, 02 Aug 2022 11:48:52: 7000000 INFO @ Tue, 02 Aug 2022 11:48:57: 13000000 INFO @ Tue, 02 Aug 2022 11:48:58: 18000000 INFO @ Tue, 02 Aug 2022 11:48:58: 8000000 INFO @ Tue, 02 Aug 2022 11:49:03: 14000000 INFO @ Tue, 02 Aug 2022 11:49:04: 19000000 INFO @ Tue, 02 Aug 2022 11:49:04: 9000000 INFO @ Tue, 02 Aug 2022 11:49:08: 15000000 INFO @ Tue, 02 Aug 2022 11:49:10: 20000000 INFO @ Tue, 02 Aug 2022 11:49:10: 10000000 INFO @ Tue, 02 Aug 2022 11:49:14: 16000000 INFO @ Tue, 02 Aug 2022 11:49:16: 11000000 INFO @ Tue, 02 Aug 2022 11:49:16: 21000000 INFO @ Tue, 02 Aug 2022 11:49:20: 17000000 INFO @ Tue, 02 Aug 2022 11:49:22: 22000000 INFO @ Tue, 02 Aug 2022 11:49:22: 12000000 INFO @ Tue, 02 Aug 2022 11:49:27: 18000000 INFO @ Tue, 02 Aug 2022 11:49:27: 13000000 INFO @ Tue, 02 Aug 2022 11:49:27: 23000000 INFO @ Tue, 02 Aug 2022 11:49:33: 19000000 INFO @ Tue, 02 Aug 2022 11:49:33: 14000000 INFO @ Tue, 02 Aug 2022 11:49:33: 24000000 INFO @ Tue, 02 Aug 2022 11:49:39: 15000000 INFO @ Tue, 02 Aug 2022 11:49:39: 25000000 INFO @ Tue, 02 Aug 2022 11:49:39: 20000000 INFO @ Tue, 02 Aug 2022 11:49:44: 16000000 INFO @ Tue, 02 Aug 2022 11:49:45: 26000000 INFO @ Tue, 02 Aug 2022 11:49:45: 21000000 INFO @ Tue, 02 Aug 2022 11:49:50: 27000000 INFO @ Tue, 02 Aug 2022 11:49:51: 17000000 INFO @ Tue, 02 Aug 2022 11:49:52: 22000000 INFO @ Tue, 02 Aug 2022 11:49:56: 28000000 INFO @ Tue, 02 Aug 2022 11:49:57: 18000000 INFO @ Tue, 02 Aug 2022 11:49:58: 23000000 INFO @ Tue, 02 Aug 2022 11:50:02: 29000000 INFO @ Tue, 02 Aug 2022 11:50:03: 19000000 INFO @ Tue, 02 Aug 2022 11:50:04: 24000000 INFO @ Tue, 02 Aug 2022 11:50:08: 30000000 INFO @ Tue, 02 Aug 2022 11:50:10: 20000000 INFO @ Tue, 02 Aug 2022 11:50:11: 25000000 INFO @ Tue, 02 Aug 2022 11:50:14: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:50:16: 21000000 INFO @ Tue, 02 Aug 2022 11:50:17: 26000000 INFO @ Tue, 02 Aug 2022 11:50:19: 32000000 INFO @ Tue, 02 Aug 2022 11:50:22: 22000000 INFO @ Tue, 02 Aug 2022 11:50:23: 27000000 INFO @ Tue, 02 Aug 2022 11:50:25: 33000000 INFO @ Tue, 02 Aug 2022 11:50:29: 23000000 INFO @ Tue, 02 Aug 2022 11:50:30: 28000000 INFO @ Tue, 02 Aug 2022 11:50:31: 34000000 INFO @ Tue, 02 Aug 2022 11:50:35: 24000000 INFO @ Tue, 02 Aug 2022 11:50:36: 29000000 INFO @ Tue, 02 Aug 2022 11:50:37: 35000000 INFO @ Tue, 02 Aug 2022 11:50:42: 25000000 INFO @ Tue, 02 Aug 2022 11:50:42: 36000000 INFO @ Tue, 02 Aug 2022 11:50:43: 30000000 INFO @ Tue, 02 Aug 2022 11:50:45: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:50:45: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:50:45: #1 total tags in treatment: 14089900 INFO @ Tue, 02 Aug 2022 11:50:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:50:45: #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 11:50:46: #1 tags after filtering in treatment: 9753275 INFO @ Tue, 02 Aug 2022 11:50:46: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 02 Aug 2022 11:50:46: #1 finished! INFO @ Tue, 02 Aug 2022 11:50:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:50:47: #2 number of paired peaks: 3197 INFO @ Tue, 02 Aug 2022 11:50:47: start model_add_line... INFO @ Tue, 02 Aug 2022 11:50:47: start X-correlation... INFO @ Tue, 02 Aug 2022 11:50:47: end of X-cor INFO @ Tue, 02 Aug 2022 11:50:47: #2 finished! INFO @ Tue, 02 Aug 2022 11:50:47: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:50:47: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:50:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05_model.r WARNING @ Tue, 02 Aug 2022 11:50:47: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:50:47: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:50:47: #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 11:50:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:50:48: 26000000 INFO @ Tue, 02 Aug 2022 11:50:49: 31000000 INFO @ Tue, 02 Aug 2022 11:50:54: 27000000 INFO @ Tue, 02 Aug 2022 11:50:55: 32000000 INFO @ Tue, 02 Aug 2022 11:51:00: 28000000 INFO @ Tue, 02 Aug 2022 11:51:02: 33000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:51:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:51:07: 29000000 INFO @ Tue, 02 Aug 2022 11:51:08: 34000000 INFO @ Tue, 02 Aug 2022 11:51:13: 30000000 INFO @ Tue, 02 Aug 2022 11:51:14: 35000000 INFO @ Tue, 02 Aug 2022 11:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.05_summits.bed INFO @ Tue, 02 Aug 2022 11:51:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17847 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:51:20: 31000000 INFO @ Tue, 02 Aug 2022 11:51:21: 36000000 INFO @ Tue, 02 Aug 2022 11:51:24: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:51:24: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:51:24: #1 total tags in treatment: 14089900 INFO @ Tue, 02 Aug 2022 11:51:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:51:24: #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 11:51:24: #1 tags after filtering in treatment: 9753275 INFO @ Tue, 02 Aug 2022 11:51:24: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 02 Aug 2022 11:51:24: #1 finished! INFO @ Tue, 02 Aug 2022 11:51:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:51:25: #2 number of paired peaks: 3197 INFO @ Tue, 02 Aug 2022 11:51:25: start model_add_line... INFO @ Tue, 02 Aug 2022 11:51:25: start X-correlation... INFO @ Tue, 02 Aug 2022 11:51:25: end of X-cor INFO @ Tue, 02 Aug 2022 11:51:25: #2 finished! INFO @ Tue, 02 Aug 2022 11:51:25: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:51:25: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10_model.r WARNING @ Tue, 02 Aug 2022 11:51:25: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:51:25: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:51:25: #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 11:51:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:51:26: 32000000 INFO @ Tue, 02 Aug 2022 11:51:32: 33000000 INFO @ Tue, 02 Aug 2022 11:51:38: 34000000 INFO @ Tue, 02 Aug 2022 11:51:43: 35000000 INFO @ Tue, 02 Aug 2022 11:51:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:51:49: 36000000 INFO @ Tue, 02 Aug 2022 11:51:52: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:51:52: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:51:52: #1 total tags in treatment: 14089900 INFO @ Tue, 02 Aug 2022 11:51:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:51:52: #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 11:51:52: #1 tags after filtering in treatment: 9753275 INFO @ Tue, 02 Aug 2022 11:51:52: #1 Redundant rate of treatment: 0.31 INFO @ Tue, 02 Aug 2022 11:51:52: #1 finished! INFO @ Tue, 02 Aug 2022 11:51:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:51:53: #2 number of paired peaks: 3197 INFO @ Tue, 02 Aug 2022 11:51:53: start model_add_line... INFO @ Tue, 02 Aug 2022 11:51:53: start X-correlation... INFO @ Tue, 02 Aug 2022 11:51:53: end of X-cor INFO @ Tue, 02 Aug 2022 11:51:53: #2 finished! INFO @ Tue, 02 Aug 2022 11:51:53: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 11:51:53: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 11:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20_model.r WARNING @ Tue, 02 Aug 2022 11:51:53: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:51:53: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 11:51:53: #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 11:51:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.10_summits.bed INFO @ Tue, 02 Aug 2022 11:51:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9286 records, 4 fields): 74 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:52:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178871/SRX12178871.20_summits.bed INFO @ Tue, 02 Aug 2022 11:52:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1630 records, 4 fields): 86 millis CompletedMACS2peakCalling