Job ID = 12265654 SRX = SRX7277055 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32650450 spots for SRR10597320/SRR10597320.sra Written 32650450 spots for SRR10597320/SRR10597320.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266039 ("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: 00:38:27 32650450 reads; of these: 32650450 (100.00%) were paired; of these: 1334913 (4.09%) aligned concordantly 0 times 9767479 (29.92%) aligned concordantly exactly 1 time 21548058 (66.00%) aligned concordantly >1 times ---- 1334913 pairs aligned concordantly 0 times; of these: 342272 (25.64%) aligned discordantly 1 time ---- 992641 pairs aligned 0 times concordantly or discordantly; of these: 1985282 mates make up the pairs; of these: 949073 (47.81%) aligned 0 times 333154 (16.78%) aligned exactly 1 time 703055 (35.41%) aligned >1 times 98.55% overall alignment rate Time searching: 00:38:27 Overall time: 00:38:28 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] 18008296 / 31570862 = 0.5704 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 08:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.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 08:49:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:49:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:49:56: 1000000 INFO @ Sat, 03 Apr 2021 08:50:02: 2000000 INFO @ Sat, 03 Apr 2021 08:50:09: 3000000 INFO @ Sat, 03 Apr 2021 08:50:15: 4000000 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 08:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.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 08:50:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:50:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:21: 5000000 INFO @ Sat, 03 Apr 2021 08:50:27: 1000000 INFO @ Sat, 03 Apr 2021 08:50:27: 6000000 INFO @ Sat, 03 Apr 2021 08:50:33: 2000000 INFO @ Sat, 03 Apr 2021 08:50:34: 7000000 INFO @ Sat, 03 Apr 2021 08:50:39: 3000000 INFO @ Sat, 03 Apr 2021 08:50:40: 8000000 INFO @ Sat, 03 Apr 2021 08:50:46: 4000000 INFO @ Sat, 03 Apr 2021 08:50:46: 9000000 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 08:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.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 08:50:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:50:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:50:53: 5000000 INFO @ Sat, 03 Apr 2021 08:50:54: 10000000 INFO @ Sat, 03 Apr 2021 08:50:57: 1000000 INFO @ Sat, 03 Apr 2021 08:50:59: 6000000 INFO @ Sat, 03 Apr 2021 08:51:02: 11000000 INFO @ Sat, 03 Apr 2021 08:51:04: 2000000 INFO @ Sat, 03 Apr 2021 08:51:05: 7000000 INFO @ Sat, 03 Apr 2021 08:51:09: 12000000 INFO @ Sat, 03 Apr 2021 08:51:11: 3000000 INFO @ Sat, 03 Apr 2021 08:51:12: 8000000 INFO @ Sat, 03 Apr 2021 08:51:17: 13000000 INFO @ Sat, 03 Apr 2021 08:51:18: 4000000 INFO @ Sat, 03 Apr 2021 08:51:19: 9000000 INFO @ Sat, 03 Apr 2021 08:51:23: 14000000 INFO @ Sat, 03 Apr 2021 08:51:25: 5000000 INFO @ Sat, 03 Apr 2021 08:51:26: 10000000 INFO @ Sat, 03 Apr 2021 08:51:30: 15000000 INFO @ Sat, 03 Apr 2021 08:51:32: 6000000 INFO @ Sat, 03 Apr 2021 08:51:34: 11000000 INFO @ Sat, 03 Apr 2021 08:51:37: 16000000 INFO @ Sat, 03 Apr 2021 08:51:38: 7000000 INFO @ Sat, 03 Apr 2021 08:51:41: 12000000 INFO @ Sat, 03 Apr 2021 08:51:43: 17000000 INFO @ Sat, 03 Apr 2021 08:51:45: 8000000 INFO @ Sat, 03 Apr 2021 08:51:48: 13000000 INFO @ Sat, 03 Apr 2021 08:51:49: 18000000 INFO @ Sat, 03 Apr 2021 08:51:52: 9000000 INFO @ Sat, 03 Apr 2021 08:51:55: 14000000 INFO @ Sat, 03 Apr 2021 08:51:55: 19000000 INFO @ Sat, 03 Apr 2021 08:51:59: 10000000 INFO @ Sat, 03 Apr 2021 08:52:01: 15000000 INFO @ Sat, 03 Apr 2021 08:52:02: 20000000 INFO @ Sat, 03 Apr 2021 08:52:07: 11000000 INFO @ Sat, 03 Apr 2021 08:52:07: 16000000 INFO @ Sat, 03 Apr 2021 08:52:08: 21000000 INFO @ Sat, 03 Apr 2021 08:52:14: 17000000 INFO @ Sat, 03 Apr 2021 08:52:14: 22000000 INFO @ Sat, 03 Apr 2021 08:52:15: 12000000 INFO @ Sat, 03 Apr 2021 08:52:20: 18000000 INFO @ Sat, 03 Apr 2021 08:52:21: 23000000 INFO @ Sat, 03 Apr 2021 08:52:22: 13000000 INFO @ Sat, 03 Apr 2021 08:52:26: 19000000 INFO @ Sat, 03 Apr 2021 08:52:27: 24000000 INFO @ Sat, 03 Apr 2021 08:52:28: 14000000 INFO @ Sat, 03 Apr 2021 08:52:32: 20000000 INFO @ Sat, 03 Apr 2021 08:52:35: 25000000 INFO @ Sat, 03 Apr 2021 08:52:35: 15000000 INFO @ Sat, 03 Apr 2021 08:52:39: 21000000 INFO @ Sat, 03 Apr 2021 08:52:42: 16000000 INFO @ Sat, 03 Apr 2021 08:52:42: 26000000 INFO @ Sat, 03 Apr 2021 08:52:45: 22000000 INFO @ Sat, 03 Apr 2021 08:52:48: 17000000 INFO @ Sat, 03 Apr 2021 08:52:49: 27000000 INFO @ Sat, 03 Apr 2021 08:52:51: 23000000 INFO @ Sat, 03 Apr 2021 08:52:54: 18000000 INFO @ Sat, 03 Apr 2021 08:52:55: 28000000 INFO @ Sat, 03 Apr 2021 08:52:57: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:52:57: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:52:57: #1 total tags in treatment: 13332307 INFO @ Sat, 03 Apr 2021 08:52:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:52:57: #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 08:52:58: 24000000 INFO @ Sat, 03 Apr 2021 08:52:58: #1 tags after filtering in treatment: 9773204 INFO @ Sat, 03 Apr 2021 08:52:58: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:52:58: #1 finished! INFO @ Sat, 03 Apr 2021 08:52:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:52:58: #2 number of paired peaks: 135 WARNING @ Sat, 03 Apr 2021 08:52:58: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 03 Apr 2021 08:52:58: start model_add_line... INFO @ Sat, 03 Apr 2021 08:52:58: start X-correlation... INFO @ Sat, 03 Apr 2021 08:52:58: end of X-cor INFO @ Sat, 03 Apr 2021 08:52:58: #2 finished! INFO @ Sat, 03 Apr 2021 08:52:58: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 08:52:58: #2 alternative fragment length(s) may be 3,53,72,593,597 bps INFO @ Sat, 03 Apr 2021 08:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05_model.r WARNING @ Sat, 03 Apr 2021 08:52:58: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:52:58: #2 You may need to consider one of the other alternative d(s): 3,53,72,593,597 WARNING @ Sat, 03 Apr 2021 08:52:58: #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 08:52:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:53:01: 19000000 INFO @ Sat, 03 Apr 2021 08:53:05: 25000000 INFO @ Sat, 03 Apr 2021 08:53:07: 20000000 INFO @ Sat, 03 Apr 2021 08:53:12: 26000000 INFO @ Sat, 03 Apr 2021 08:53:13: 21000000 INFO @ Sat, 03 Apr 2021 08:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:53:18: 27000000 INFO @ Sat, 03 Apr 2021 08:53:19: 22000000 INFO @ Sat, 03 Apr 2021 08:53:25: 28000000 INFO @ Sat, 03 Apr 2021 08:53:25: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:53:27: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:53:27: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:53:27: #1 total tags in treatment: 13332307 INFO @ Sat, 03 Apr 2021 08:53:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:53:27: #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 08:53:27: #1 tags after filtering in treatment: 9773204 INFO @ Sat, 03 Apr 2021 08:53:27: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:53:27: #1 finished! INFO @ Sat, 03 Apr 2021 08:53:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:53:28: #2 number of paired peaks: 135 WARNING @ Sat, 03 Apr 2021 08:53:28: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 03 Apr 2021 08:53:28: start model_add_line... INFO @ Sat, 03 Apr 2021 08:53:28: start X-correlation... INFO @ Sat, 03 Apr 2021 08:53:28: end of X-cor INFO @ Sat, 03 Apr 2021 08:53:28: #2 finished! INFO @ Sat, 03 Apr 2021 08:53:28: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 08:53:28: #2 alternative fragment length(s) may be 3,53,72,593,597 bps INFO @ Sat, 03 Apr 2021 08:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10_model.r WARNING @ Sat, 03 Apr 2021 08:53:28: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:53:28: #2 You may need to consider one of the other alternative d(s): 3,53,72,593,597 WARNING @ Sat, 03 Apr 2021 08:53:28: #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 08:53:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.05_summits.bed INFO @ Sat, 03 Apr 2021 08:53:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2751 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:53:31: 24000000 INFO @ Sat, 03 Apr 2021 08:53:38: 25000000 INFO @ Sat, 03 Apr 2021 08:53:45: 26000000 INFO @ Sat, 03 Apr 2021 08:53:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:53:51: 27000000 INFO @ Sat, 03 Apr 2021 08:53:57: 28000000 INFO @ Sat, 03 Apr 2021 08:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.10_summits.bed INFO @ Sat, 03 Apr 2021 08:53:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:53:58: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:53:58: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:53:58: #1 total tags in treatment: 13332307 INFO @ Sat, 03 Apr 2021 08:53:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:53:58: #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 08:53:59: #1 tags after filtering in treatment: 9773204 INFO @ Sat, 03 Apr 2021 08:53:59: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:53:59: #1 finished! INFO @ Sat, 03 Apr 2021 08:53:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:53:59: #2 number of paired peaks: 135 WARNING @ Sat, 03 Apr 2021 08:53:59: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 03 Apr 2021 08:53:59: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:00: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:00: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:00: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:00: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 08:54:00: #2 alternative fragment length(s) may be 3,53,72,593,597 bps INFO @ Sat, 03 Apr 2021 08:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20_model.r WARNING @ Sat, 03 Apr 2021 08:54:00: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:54:00: #2 You may need to consider one of the other alternative d(s): 3,53,72,593,597 WARNING @ Sat, 03 Apr 2021 08:54:00: #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 08:54:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277055/SRX7277055.20_summits.bed INFO @ Sat, 03 Apr 2021 08:54:28: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling