Job ID = 16438093 SRX = SRX10031705 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41058713 spots for SRR13634475/SRR13634475.sra Written 41058713 spots for SRR13634475/SRR13634475.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438527 ("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: 00:17:33 41058713 reads; of these: 41058713 (100.00%) were unpaired; of these: 1476203 (3.60%) aligned 0 times 32758465 (79.78%) aligned exactly 1 time 6824045 (16.62%) aligned >1 times 96.40% overall alignment rate Time searching: 00:17:33 Overall time: 00:17:33 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_rmdupse_core] 7300789 / 39582510 = 0.1844 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 14:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.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 14:03:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:03:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:03:58: 1000000 INFO @ Tue, 02 Aug 2022 14:04:05: 2000000 INFO @ Tue, 02 Aug 2022 14:04:12: 3000000 INFO @ Tue, 02 Aug 2022 14:04:19: 4000000 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 14:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.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 14:04:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:04:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:04:26: 5000000 INFO @ Tue, 02 Aug 2022 14:04:28: 1000000 INFO @ Tue, 02 Aug 2022 14:04:33: 6000000 INFO @ Tue, 02 Aug 2022 14:04:35: 2000000 INFO @ Tue, 02 Aug 2022 14:04:40: 7000000 INFO @ Tue, 02 Aug 2022 14:04:42: 3000000 INFO @ Tue, 02 Aug 2022 14:04:47: 8000000 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 14:04:49: 4000000 INFO @ Tue, 02 Aug 2022 14:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.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 14:04:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:04:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:04:54: 9000000 INFO @ Tue, 02 Aug 2022 14:04:56: 5000000 INFO @ Tue, 02 Aug 2022 14:04:58: 1000000 INFO @ Tue, 02 Aug 2022 14:05:01: 10000000 INFO @ Tue, 02 Aug 2022 14:05:03: 6000000 INFO @ Tue, 02 Aug 2022 14:05:05: 2000000 INFO @ Tue, 02 Aug 2022 14:05:08: 11000000 INFO @ Tue, 02 Aug 2022 14:05:10: 7000000 INFO @ Tue, 02 Aug 2022 14:05:12: 3000000 INFO @ Tue, 02 Aug 2022 14:05:16: 12000000 INFO @ Tue, 02 Aug 2022 14:05:17: 8000000 INFO @ Tue, 02 Aug 2022 14:05:19: 4000000 INFO @ Tue, 02 Aug 2022 14:05:23: 13000000 INFO @ Tue, 02 Aug 2022 14:05:24: 9000000 INFO @ Tue, 02 Aug 2022 14:05:26: 5000000 INFO @ Tue, 02 Aug 2022 14:05:30: 14000000 INFO @ Tue, 02 Aug 2022 14:05:31: 10000000 INFO @ Tue, 02 Aug 2022 14:05:33: 6000000 INFO @ Tue, 02 Aug 2022 14:05:37: 15000000 INFO @ Tue, 02 Aug 2022 14:05:38: 11000000 INFO @ Tue, 02 Aug 2022 14:05:40: 7000000 INFO @ Tue, 02 Aug 2022 14:05:44: 16000000 INFO @ Tue, 02 Aug 2022 14:05:45: 12000000 INFO @ Tue, 02 Aug 2022 14:05:47: 8000000 INFO @ Tue, 02 Aug 2022 14:05:51: 17000000 INFO @ Tue, 02 Aug 2022 14:05:52: 13000000 INFO @ Tue, 02 Aug 2022 14:05:54: 9000000 INFO @ Tue, 02 Aug 2022 14:05:57: 18000000 INFO @ Tue, 02 Aug 2022 14:05:59: 14000000 INFO @ Tue, 02 Aug 2022 14:06:01: 10000000 INFO @ Tue, 02 Aug 2022 14:06:04: 19000000 INFO @ Tue, 02 Aug 2022 14:06:06: 15000000 INFO @ Tue, 02 Aug 2022 14:06:08: 11000000 INFO @ Tue, 02 Aug 2022 14:06:11: 20000000 INFO @ Tue, 02 Aug 2022 14:06:13: 16000000 INFO @ Tue, 02 Aug 2022 14:06:14: 12000000 INFO @ Tue, 02 Aug 2022 14:06:18: 21000000 INFO @ Tue, 02 Aug 2022 14:06:19: 17000000 INFO @ Tue, 02 Aug 2022 14:06:21: 13000000 INFO @ Tue, 02 Aug 2022 14:06:25: 22000000 INFO @ Tue, 02 Aug 2022 14:06:26: 18000000 INFO @ Tue, 02 Aug 2022 14:06:28: 14000000 INFO @ Tue, 02 Aug 2022 14:06:32: 23000000 INFO @ Tue, 02 Aug 2022 14:06:33: 19000000 INFO @ Tue, 02 Aug 2022 14:06:35: 15000000 INFO @ Tue, 02 Aug 2022 14:06:39: 24000000 INFO @ Tue, 02 Aug 2022 14:06:40: 20000000 INFO @ Tue, 02 Aug 2022 14:06:42: 16000000 INFO @ Tue, 02 Aug 2022 14:06:46: 25000000 INFO @ Tue, 02 Aug 2022 14:06:47: 21000000 INFO @ Tue, 02 Aug 2022 14:06:49: 17000000 INFO @ Tue, 02 Aug 2022 14:06:53: 26000000 INFO @ Tue, 02 Aug 2022 14:06:53: 22000000 INFO @ Tue, 02 Aug 2022 14:06:56: 18000000 INFO @ Tue, 02 Aug 2022 14:07:00: 23000000 INFO @ Tue, 02 Aug 2022 14:07:00: 27000000 INFO @ Tue, 02 Aug 2022 14:07:03: 19000000 INFO @ Tue, 02 Aug 2022 14:07:07: 24000000 INFO @ Tue, 02 Aug 2022 14:07:07: 28000000 INFO @ Tue, 02 Aug 2022 14:07:10: 20000000 INFO @ Tue, 02 Aug 2022 14:07:14: 25000000 INFO @ Tue, 02 Aug 2022 14:07:14: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:07:17: 21000000 INFO @ Tue, 02 Aug 2022 14:07:21: 26000000 INFO @ Tue, 02 Aug 2022 14:07:21: 30000000 INFO @ Tue, 02 Aug 2022 14:07:24: 22000000 INFO @ Tue, 02 Aug 2022 14:07:28: 27000000 INFO @ Tue, 02 Aug 2022 14:07:28: 31000000 INFO @ Tue, 02 Aug 2022 14:07:31: 23000000 INFO @ Tue, 02 Aug 2022 14:07:35: 28000000 INFO @ Tue, 02 Aug 2022 14:07:35: 32000000 INFO @ Tue, 02 Aug 2022 14:07:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:07:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:07:37: #1 total tags in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:07:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:07:37: #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 14:07:38: 24000000 INFO @ Tue, 02 Aug 2022 14:07:38: #1 tags after filtering in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:07:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:07:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:07:40: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 14:07:40: 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 @ Tue, 02 Aug 2022 14:07:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:07:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:07:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:07:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:07:40: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:07:40: #2 alternative fragment length(s) may be 2,76,203,334,357,505,521,550,576 bps INFO @ Tue, 02 Aug 2022 14:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05_model.r WARNING @ Tue, 02 Aug 2022 14:07:40: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:07:40: #2 You may need to consider one of the other alternative d(s): 2,76,203,334,357,505,521,550,576 WARNING @ Tue, 02 Aug 2022 14:07:40: #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 14:07:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:07:41: 29000000 INFO @ Tue, 02 Aug 2022 14:07:44: 25000000 INFO @ Tue, 02 Aug 2022 14:07:48: 30000000 INFO @ Tue, 02 Aug 2022 14:07:51: 26000000 INFO @ Tue, 02 Aug 2022 14:07:55: 31000000 INFO @ Tue, 02 Aug 2022 14:07:58: 27000000 INFO @ Tue, 02 Aug 2022 14:08:02: 32000000 INFO @ Tue, 02 Aug 2022 14:08:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:08:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:08:04: #1 total tags in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:08:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:04: #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 14:08:04: #1 tags after filtering in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:08:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:05: 28000000 INFO @ Tue, 02 Aug 2022 14:08:06: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 14:08:06: 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 @ Tue, 02 Aug 2022 14:08:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:06: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:08:06: #2 alternative fragment length(s) may be 2,76,203,334,357,505,521,550,576 bps INFO @ Tue, 02 Aug 2022 14:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10_model.r WARNING @ Tue, 02 Aug 2022 14:08:06: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:08:06: #2 You may need to consider one of the other alternative d(s): 2,76,203,334,357,505,521,550,576 WARNING @ Tue, 02 Aug 2022 14:08:06: #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 14:08:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:11: 29000000 INFO @ Tue, 02 Aug 2022 14:08:18: 30000000 INFO @ Tue, 02 Aug 2022 14:08:24: 31000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:08:30: 32000000 INFO @ Tue, 02 Aug 2022 14:08:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:08:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:08:32: #1 total tags in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:08:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:32: #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 14:08:33: #1 tags after filtering in treatment: 32281721 INFO @ Tue, 02 Aug 2022 14:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:08:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:35: #2 number of paired peaks: 123 WARNING @ Tue, 02 Aug 2022 14:08:35: 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 @ Tue, 02 Aug 2022 14:08:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:35: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 14:08:35: #2 alternative fragment length(s) may be 2,76,203,334,357,505,521,550,576 bps INFO @ Tue, 02 Aug 2022 14:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20_model.r WARNING @ Tue, 02 Aug 2022 14:08:35: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:08:35: #2 You may need to consider one of the other alternative d(s): 2,76,203,334,357,505,521,550,576 WARNING @ Tue, 02 Aug 2022 14:08:35: #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 14:08:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.05_summits.bed INFO @ Tue, 02 Aug 2022 14:08:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4246 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:08:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:09:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:09:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:09:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.10_summits.bed INFO @ Tue, 02 Aug 2022 14:09:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1986 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:09:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031705/SRX10031705.20_summits.bed INFO @ Tue, 02 Aug 2022 14:09:49: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (638 records, 4 fields): 301 millis CompletedMACS2peakCalling