Job ID = 12265644 SRX = SRX7277048 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30035062 spots for SRR10597313/SRR10597313.sra Written 30035062 spots for SRR10597313/SRR10597313.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266151 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:47:04 30035062 reads; of these: 30035062 (100.00%) were paired; of these: 1770284 (5.89%) aligned concordantly 0 times 13249260 (44.11%) aligned concordantly exactly 1 time 15015518 (49.99%) aligned concordantly >1 times ---- 1770284 pairs aligned concordantly 0 times; of these: 576204 (32.55%) aligned discordantly 1 time ---- 1194080 pairs aligned 0 times concordantly or discordantly; of these: 2388160 mates make up the pairs; of these: 1187254 (49.71%) aligned 0 times 454692 (19.04%) aligned exactly 1 time 746214 (31.25%) aligned >1 times 98.02% overall alignment rate Time searching: 00:47:05 Overall time: 00:47:05 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 16 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] 11260576 / 28732300 = 0.3919 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 08:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.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 08:57:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:57:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:57:12: 1000000 INFO @ Sat, 03 Apr 2021 08:57:16: 2000000 INFO @ Sat, 03 Apr 2021 08:57:20: 3000000 INFO @ Sat, 03 Apr 2021 08:57:24: 4000000 INFO @ Sat, 03 Apr 2021 08:57:29: 5000000 INFO @ Sat, 03 Apr 2021 08:57:33: 6000000 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 08:57:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.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 08:57:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:57:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:57:38: 7000000 INFO @ Sat, 03 Apr 2021 08:57:41: 1000000 INFO @ Sat, 03 Apr 2021 08:57:42: 8000000 INFO @ Sat, 03 Apr 2021 08:57:45: 2000000 INFO @ Sat, 03 Apr 2021 08:57:46: 9000000 INFO @ Sat, 03 Apr 2021 08:57:49: 3000000 INFO @ Sat, 03 Apr 2021 08:57:50: 10000000 INFO @ Sat, 03 Apr 2021 08:57:54: 4000000 INFO @ Sat, 03 Apr 2021 08:57:54: 11000000 INFO @ Sat, 03 Apr 2021 08:57:58: 5000000 INFO @ Sat, 03 Apr 2021 08:57:58: 12000000 INFO @ Sat, 03 Apr 2021 08:58:02: 6000000 INFO @ Sat, 03 Apr 2021 08:58:02: 13000000 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 08:58:06: 7000000 INFO @ Sat, 03 Apr 2021 08:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.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 08:58:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:58:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:58:07: 14000000 INFO @ Sat, 03 Apr 2021 08:58:11: 8000000 INFO @ Sat, 03 Apr 2021 08:58:11: 1000000 INFO @ Sat, 03 Apr 2021 08:58:11: 15000000 INFO @ Sat, 03 Apr 2021 08:58:15: 9000000 INFO @ Sat, 03 Apr 2021 08:58:16: 2000000 INFO @ Sat, 03 Apr 2021 08:58:16: 16000000 INFO @ Sat, 03 Apr 2021 08:58:19: 10000000 INFO @ Sat, 03 Apr 2021 08:58:20: 3000000 INFO @ Sat, 03 Apr 2021 08:58:20: 17000000 INFO @ Sat, 03 Apr 2021 08:58:23: 11000000 INFO @ Sat, 03 Apr 2021 08:58:24: 4000000 INFO @ Sat, 03 Apr 2021 08:58:24: 18000000 INFO @ Sat, 03 Apr 2021 08:58:28: 12000000 INFO @ Sat, 03 Apr 2021 08:58:29: 5000000 INFO @ Sat, 03 Apr 2021 08:58:29: 19000000 INFO @ Sat, 03 Apr 2021 08:58:32: 13000000 INFO @ Sat, 03 Apr 2021 08:58:33: 6000000 INFO @ Sat, 03 Apr 2021 08:58:33: 20000000 INFO @ Sat, 03 Apr 2021 08:58:36: 14000000 INFO @ Sat, 03 Apr 2021 08:58:37: 7000000 INFO @ Sat, 03 Apr 2021 08:58:37: 21000000 INFO @ Sat, 03 Apr 2021 08:58:40: 15000000 INFO @ Sat, 03 Apr 2021 08:58:41: 8000000 INFO @ Sat, 03 Apr 2021 08:58:42: 22000000 INFO @ Sat, 03 Apr 2021 08:58:44: 16000000 INFO @ Sat, 03 Apr 2021 08:58:46: 9000000 INFO @ Sat, 03 Apr 2021 08:58:46: 23000000 INFO @ Sat, 03 Apr 2021 08:58:48: 17000000 INFO @ Sat, 03 Apr 2021 08:58:50: 24000000 INFO @ Sat, 03 Apr 2021 08:58:50: 10000000 INFO @ Sat, 03 Apr 2021 08:58:52: 18000000 INFO @ Sat, 03 Apr 2021 08:58:54: 25000000 INFO @ Sat, 03 Apr 2021 08:58:55: 11000000 INFO @ Sat, 03 Apr 2021 08:58:57: 19000000 INFO @ Sat, 03 Apr 2021 08:58:58: 26000000 INFO @ Sat, 03 Apr 2021 08:58:59: 12000000 INFO @ Sat, 03 Apr 2021 08:59:01: 20000000 INFO @ Sat, 03 Apr 2021 08:59:02: 27000000 INFO @ Sat, 03 Apr 2021 08:59:03: 13000000 INFO @ Sat, 03 Apr 2021 08:59:05: 21000000 INFO @ Sat, 03 Apr 2021 08:59:06: 28000000 INFO @ Sat, 03 Apr 2021 08:59:08: 14000000 INFO @ Sat, 03 Apr 2021 08:59:10: 22000000 INFO @ Sat, 03 Apr 2021 08:59:11: 29000000 INFO @ Sat, 03 Apr 2021 08:59:13: 15000000 INFO @ Sat, 03 Apr 2021 08:59:14: 23000000 INFO @ Sat, 03 Apr 2021 08:59:16: 30000000 INFO @ Sat, 03 Apr 2021 08:59:17: 16000000 INFO @ Sat, 03 Apr 2021 08:59:18: 24000000 INFO @ Sat, 03 Apr 2021 08:59:20: 31000000 INFO @ Sat, 03 Apr 2021 08:59:21: 17000000 INFO @ Sat, 03 Apr 2021 08:59:22: 25000000 INFO @ Sat, 03 Apr 2021 08:59:24: 32000000 INFO @ Sat, 03 Apr 2021 08:59:26: 18000000 INFO @ Sat, 03 Apr 2021 08:59:26: 26000000 INFO @ Sat, 03 Apr 2021 08:59:29: 33000000 INFO @ Sat, 03 Apr 2021 08:59:30: 27000000 INFO @ Sat, 03 Apr 2021 08:59:31: 19000000 INFO @ Sat, 03 Apr 2021 08:59:33: 34000000 INFO @ Sat, 03 Apr 2021 08:59:34: 28000000 INFO @ Sat, 03 Apr 2021 08:59:35: 20000000 INFO @ Sat, 03 Apr 2021 08:59:38: 35000000 INFO @ Sat, 03 Apr 2021 08:59:38: 29000000 INFO @ Sat, 03 Apr 2021 08:59:40: 21000000 INFO @ Sat, 03 Apr 2021 08:59:42: 30000000 INFO @ Sat, 03 Apr 2021 08:59:43: 36000000 INFO @ Sat, 03 Apr 2021 08:59:44: 22000000 INFO @ Sat, 03 Apr 2021 08:59:44: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:59:44: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:59:44: #1 total tags in treatment: 17054332 INFO @ Sat, 03 Apr 2021 08:59:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:59:44: #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 08:59:45: #1 tags after filtering in treatment: 13173120 INFO @ Sat, 03 Apr 2021 08:59:45: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:59:45: #1 finished! INFO @ Sat, 03 Apr 2021 08:59:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:59:46: #2 number of paired peaks: 123 WARNING @ Sat, 03 Apr 2021 08:59:46: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 03 Apr 2021 08:59:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:59:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:59:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:59:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:59:46: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 08:59:46: #2 alternative fragment length(s) may be 3,51,69,90,580,598 bps INFO @ Sat, 03 Apr 2021 08:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05_model.r WARNING @ Sat, 03 Apr 2021 08:59:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:59:46: #2 You may need to consider one of the other alternative d(s): 3,51,69,90,580,598 WARNING @ Sat, 03 Apr 2021 08:59:46: #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 08:59:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:59:47: 31000000 INFO @ Sat, 03 Apr 2021 08:59:49: 23000000 INFO @ Sat, 03 Apr 2021 08:59:51: 32000000 INFO @ Sat, 03 Apr 2021 08:59:52: 24000000 INFO @ Sat, 03 Apr 2021 08:59:55: 33000000 INFO @ Sat, 03 Apr 2021 08:59:56: 25000000 INFO @ Sat, 03 Apr 2021 08:59:59: 34000000 INFO @ Sat, 03 Apr 2021 09:00:00: 26000000 INFO @ Sat, 03 Apr 2021 09:00:03: 35000000 INFO @ Sat, 03 Apr 2021 09:00:04: 27000000 INFO @ Sat, 03 Apr 2021 09:00:08: 36000000 INFO @ Sat, 03 Apr 2021 09:00:08: 28000000 INFO @ Sat, 03 Apr 2021 09:00:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:00:09: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:00:09: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:00:09: #1 total tags in treatment: 17054332 INFO @ Sat, 03 Apr 2021 09:00:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:00:09: #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 09:00:10: #1 tags after filtering in treatment: 13173120 INFO @ Sat, 03 Apr 2021 09:00:10: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 09:00:10: #1 finished! INFO @ Sat, 03 Apr 2021 09:00:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:00:11: #2 number of paired peaks: 123 WARNING @ Sat, 03 Apr 2021 09:00:11: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 03 Apr 2021 09:00:11: start model_add_line... INFO @ Sat, 03 Apr 2021 09:00:11: start X-correlation... INFO @ Sat, 03 Apr 2021 09:00:11: end of X-cor INFO @ Sat, 03 Apr 2021 09:00:11: #2 finished! INFO @ Sat, 03 Apr 2021 09:00:11: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 09:00:11: #2 alternative fragment length(s) may be 3,51,69,90,580,598 bps INFO @ Sat, 03 Apr 2021 09:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10_model.r WARNING @ Sat, 03 Apr 2021 09:00:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:00:11: #2 You may need to consider one of the other alternative d(s): 3,51,69,90,580,598 WARNING @ Sat, 03 Apr 2021 09:00:11: #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 09:00:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:00:12: 29000000 INFO @ Sat, 03 Apr 2021 09:00:16: 30000000 INFO @ Sat, 03 Apr 2021 09:00:20: 31000000 INFO @ Sat, 03 Apr 2021 09:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.05_summits.bed INFO @ Sat, 03 Apr 2021 09:00:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3086 records, 4 fields): 301 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:00:24: 32000000 INFO @ Sat, 03 Apr 2021 09:00:28: 33000000 INFO @ Sat, 03 Apr 2021 09:00:32: 34000000 INFO @ Sat, 03 Apr 2021 09:00:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:00:36: 35000000 INFO @ Sat, 03 Apr 2021 09:00:40: 36000000 INFO @ Sat, 03 Apr 2021 09:00:42: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:00:42: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:00:42: #1 total tags in treatment: 17054332 INFO @ Sat, 03 Apr 2021 09:00:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:00:42: #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 09:00:42: #1 tags after filtering in treatment: 13173120 INFO @ Sat, 03 Apr 2021 09:00:42: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 09:00:42: #1 finished! INFO @ Sat, 03 Apr 2021 09:00:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:00:43: #2 number of paired peaks: 123 WARNING @ Sat, 03 Apr 2021 09:00:43: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 03 Apr 2021 09:00:43: start model_add_line... INFO @ Sat, 03 Apr 2021 09:00:43: start X-correlation... INFO @ Sat, 03 Apr 2021 09:00:43: end of X-cor INFO @ Sat, 03 Apr 2021 09:00:43: #2 finished! INFO @ Sat, 03 Apr 2021 09:00:43: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 09:00:43: #2 alternative fragment length(s) may be 3,51,69,90,580,598 bps INFO @ Sat, 03 Apr 2021 09:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20_model.r WARNING @ Sat, 03 Apr 2021 09:00:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:00:44: #2 You may need to consider one of the other alternative d(s): 3,51,69,90,580,598 WARNING @ Sat, 03 Apr 2021 09:00:44: #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 09:00:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.10_summits.bed INFO @ Sat, 03 Apr 2021 09:00:48: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (900 records, 4 fields): 431 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:01:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277048/SRX7277048.20_summits.bed INFO @ Sat, 03 Apr 2021 09:01:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (286 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。