Job ID = 6626440 SRX = ERX088869 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 149789918 spots for ERR111438/ERR111438.sra Written 149789918 spots for ERR111438/ERR111438.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626712 ("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: 00:35:40 149789918 reads; of these: 149789918 (100.00%) were unpaired; of these: 26640473 (17.79%) aligned 0 times 102503277 (68.43%) aligned exactly 1 time 20646168 (13.78%) aligned >1 times 82.21% overall alignment rate Time searching: 00:35:40 Overall time: 00:35:40 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 52 files... [bam_rmdupse_core] 81321545 / 123149445 = 0.6603 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.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, 14 Jul 2020 08:08:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:08:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:08:49: 1000000 INFO @ Tue, 14 Jul 2020 08:08:55: 2000000 INFO @ Tue, 14 Jul 2020 08:09:02: 3000000 INFO @ Tue, 14 Jul 2020 08:09:09: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.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, 14 Jul 2020 08:09:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:09:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:09:17: 5000000 INFO @ Tue, 14 Jul 2020 08:09:19: 1000000 INFO @ Tue, 14 Jul 2020 08:09:24: 6000000 INFO @ Tue, 14 Jul 2020 08:09:26: 2000000 INFO @ Tue, 14 Jul 2020 08:09:31: 7000000 INFO @ Tue, 14 Jul 2020 08:09:33: 3000000 INFO @ Tue, 14 Jul 2020 08:09:38: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:09:41: 4000000 INFO @ Tue, 14 Jul 2020 08:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.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, 14 Jul 2020 08:09:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:09:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:09:46: 9000000 INFO @ Tue, 14 Jul 2020 08:09:48: 5000000 INFO @ Tue, 14 Jul 2020 08:09:50: 1000000 INFO @ Tue, 14 Jul 2020 08:09:53: 10000000 INFO @ Tue, 14 Jul 2020 08:09:55: 6000000 INFO @ Tue, 14 Jul 2020 08:09:57: 2000000 INFO @ Tue, 14 Jul 2020 08:10:00: 11000000 INFO @ Tue, 14 Jul 2020 08:10:02: 7000000 INFO @ Tue, 14 Jul 2020 08:10:05: 3000000 INFO @ Tue, 14 Jul 2020 08:10:07: 12000000 INFO @ Tue, 14 Jul 2020 08:10:09: 8000000 INFO @ Tue, 14 Jul 2020 08:10:12: 4000000 INFO @ Tue, 14 Jul 2020 08:10:13: 13000000 INFO @ Tue, 14 Jul 2020 08:10:16: 9000000 INFO @ Tue, 14 Jul 2020 08:10:19: 5000000 INFO @ Tue, 14 Jul 2020 08:10:20: 14000000 INFO @ Tue, 14 Jul 2020 08:10:23: 10000000 INFO @ Tue, 14 Jul 2020 08:10:25: 6000000 INFO @ Tue, 14 Jul 2020 08:10:27: 15000000 INFO @ Tue, 14 Jul 2020 08:10:30: 11000000 INFO @ Tue, 14 Jul 2020 08:10:32: 7000000 INFO @ Tue, 14 Jul 2020 08:10:33: 16000000 INFO @ Tue, 14 Jul 2020 08:10:36: 12000000 INFO @ Tue, 14 Jul 2020 08:10:39: 8000000 INFO @ Tue, 14 Jul 2020 08:10:40: 17000000 INFO @ Tue, 14 Jul 2020 08:10:43: 13000000 INFO @ Tue, 14 Jul 2020 08:10:45: 9000000 INFO @ Tue, 14 Jul 2020 08:10:46: 18000000 INFO @ Tue, 14 Jul 2020 08:10:50: 14000000 INFO @ Tue, 14 Jul 2020 08:10:52: 10000000 INFO @ Tue, 14 Jul 2020 08:10:53: 19000000 INFO @ Tue, 14 Jul 2020 08:10:57: 15000000 INFO @ Tue, 14 Jul 2020 08:10:58: 11000000 INFO @ Tue, 14 Jul 2020 08:11:00: 20000000 INFO @ Tue, 14 Jul 2020 08:11:03: 16000000 INFO @ Tue, 14 Jul 2020 08:11:05: 12000000 INFO @ Tue, 14 Jul 2020 08:11:07: 21000000 INFO @ Tue, 14 Jul 2020 08:11:10: 17000000 INFO @ Tue, 14 Jul 2020 08:11:12: 13000000 INFO @ Tue, 14 Jul 2020 08:11:14: 22000000 INFO @ Tue, 14 Jul 2020 08:11:17: 18000000 INFO @ Tue, 14 Jul 2020 08:11:20: 14000000 INFO @ Tue, 14 Jul 2020 08:11:21: 23000000 INFO @ Tue, 14 Jul 2020 08:11:24: 19000000 INFO @ Tue, 14 Jul 2020 08:11:28: 24000000 INFO @ Tue, 14 Jul 2020 08:11:28: 15000000 INFO @ Tue, 14 Jul 2020 08:11:31: 20000000 INFO @ Tue, 14 Jul 2020 08:11:34: 25000000 INFO @ Tue, 14 Jul 2020 08:11:36: 16000000 INFO @ Tue, 14 Jul 2020 08:11:38: 21000000 INFO @ Tue, 14 Jul 2020 08:11:41: 26000000 INFO @ Tue, 14 Jul 2020 08:11:44: 22000000 INFO @ Tue, 14 Jul 2020 08:11:45: 17000000 INFO @ Tue, 14 Jul 2020 08:11:48: 27000000 INFO @ Tue, 14 Jul 2020 08:11:51: 23000000 INFO @ Tue, 14 Jul 2020 08:11:53: 18000000 INFO @ Tue, 14 Jul 2020 08:11:54: 28000000 INFO @ Tue, 14 Jul 2020 08:11:58: 24000000 INFO @ Tue, 14 Jul 2020 08:12:01: 29000000 INFO @ Tue, 14 Jul 2020 08:12:01: 19000000 INFO @ Tue, 14 Jul 2020 08:12:04: 25000000 INFO @ Tue, 14 Jul 2020 08:12:07: 30000000 INFO @ Tue, 14 Jul 2020 08:12:09: 20000000 INFO @ Tue, 14 Jul 2020 08:12:11: 26000000 INFO @ Tue, 14 Jul 2020 08:12:14: 31000000 INFO @ Tue, 14 Jul 2020 08:12:17: 27000000 INFO @ Tue, 14 Jul 2020 08:12:18: 21000000 INFO @ Tue, 14 Jul 2020 08:12:20: 32000000 INFO @ Tue, 14 Jul 2020 08:12:24: 28000000 INFO @ Tue, 14 Jul 2020 08:12:26: 22000000 INFO @ Tue, 14 Jul 2020 08:12:27: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:12:30: 29000000 INFO @ Tue, 14 Jul 2020 08:12:34: 34000000 INFO @ Tue, 14 Jul 2020 08:12:34: 23000000 INFO @ Tue, 14 Jul 2020 08:12:36: 30000000 INFO @ Tue, 14 Jul 2020 08:12:41: 35000000 INFO @ Tue, 14 Jul 2020 08:12:42: 24000000 INFO @ Tue, 14 Jul 2020 08:12:43: 31000000 INFO @ Tue, 14 Jul 2020 08:12:47: 36000000 INFO @ Tue, 14 Jul 2020 08:12:49: 32000000 INFO @ Tue, 14 Jul 2020 08:12:50: 25000000 INFO @ Tue, 14 Jul 2020 08:12:54: 37000000 INFO @ Tue, 14 Jul 2020 08:12:56: 33000000 INFO @ Tue, 14 Jul 2020 08:12:58: 26000000 INFO @ Tue, 14 Jul 2020 08:13:01: 38000000 INFO @ Tue, 14 Jul 2020 08:13:03: 34000000 INFO @ Tue, 14 Jul 2020 08:13:07: 27000000 INFO @ Tue, 14 Jul 2020 08:13:08: 39000000 INFO @ Tue, 14 Jul 2020 08:13:09: 35000000 INFO @ Tue, 14 Jul 2020 08:13:14: 28000000 INFO @ Tue, 14 Jul 2020 08:13:15: 40000000 INFO @ Tue, 14 Jul 2020 08:13:16: 36000000 INFO @ Tue, 14 Jul 2020 08:13:22: 41000000 INFO @ Tue, 14 Jul 2020 08:13:23: 29000000 INFO @ Tue, 14 Jul 2020 08:13:23: 37000000 INFO @ Tue, 14 Jul 2020 08:13:28: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:13:28: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:13:28: #1 total tags in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:13:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:13:28: #1 tags after filtering in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:13:28: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:29: 38000000 INFO @ Tue, 14 Jul 2020 08:13:31: 30000000 INFO @ Tue, 14 Jul 2020 08:13:31: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 08:13:31: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 08:13:31: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:31: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:31: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:31: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:31: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 08:13:31: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 14 Jul 2020 08:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05_model.r WARNING @ Tue, 14 Jul 2020 08:13:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:31: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 14 Jul 2020 08:13:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:13:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:13:36: 39000000 INFO @ Tue, 14 Jul 2020 08:13:39: 31000000 INFO @ Tue, 14 Jul 2020 08:13:42: 40000000 INFO @ Tue, 14 Jul 2020 08:13:47: 32000000 INFO @ Tue, 14 Jul 2020 08:13:49: 41000000 INFO @ Tue, 14 Jul 2020 08:13:54: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:13:54: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:13:54: #1 total tags in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:13:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:13:55: 33000000 INFO @ Tue, 14 Jul 2020 08:13:55: #1 tags after filtering in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:13:55: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:58: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 08:13:58: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 08:13:58: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:58: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:58: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:58: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:58: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 08:13:58: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 14 Jul 2020 08:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10_model.r WARNING @ Tue, 14 Jul 2020 08:13:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:58: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 14 Jul 2020 08:13:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:13:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:14:03: 34000000 INFO @ Tue, 14 Jul 2020 08:14:10: 35000000 INFO @ Tue, 14 Jul 2020 08:14:16: 36000000 INFO @ Tue, 14 Jul 2020 08:14:22: 37000000 INFO @ Tue, 14 Jul 2020 08:14:28: 38000000 INFO @ Tue, 14 Jul 2020 08:14:34: 39000000 INFO @ Tue, 14 Jul 2020 08:14:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:14:40: 40000000 INFO @ Tue, 14 Jul 2020 08:14:46: 41000000 INFO @ Tue, 14 Jul 2020 08:14:52: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:14:52: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:14:52: #1 total tags in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:14:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:14:52: #1 tags after filtering in treatment: 41827900 INFO @ Tue, 14 Jul 2020 08:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:14:52: #1 finished! INFO @ Tue, 14 Jul 2020 08:14:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:14:55: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 08:14:55: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 08:14:55: start model_add_line... INFO @ Tue, 14 Jul 2020 08:14:56: start X-correlation... INFO @ Tue, 14 Jul 2020 08:14:56: end of X-cor INFO @ Tue, 14 Jul 2020 08:14:56: #2 finished! INFO @ Tue, 14 Jul 2020 08:14:56: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 08:14:56: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 14 Jul 2020 08:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20_model.r WARNING @ Tue, 14 Jul 2020 08:14:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:14:56: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 14 Jul 2020 08:14:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:14:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:15:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:15:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.05_summits.bed INFO @ Tue, 14 Jul 2020 08:15:12: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (39254 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.10_summits.bed INFO @ Tue, 14 Jul 2020 08:15:35: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (19956 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088869/ERX088869.20_summits.bed INFO @ Tue, 14 Jul 2020 08:16:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6632 records, 4 fields): 7 millis CompletedMACS2peakCalling