Job ID = 16439428 SRX = SRX11245084 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21074333 spots for SRR14932349/SRR14932349.sra Written 21074333 spots for SRR14932349/SRR14932349.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439857 ("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: 01:06:52 21074333 reads; of these: 21074333 (100.00%) were paired; of these: 12551952 (59.56%) aligned concordantly 0 times 7066500 (33.53%) aligned concordantly exactly 1 time 1455881 (6.91%) aligned concordantly >1 times ---- 12551952 pairs aligned concordantly 0 times; of these: 1673622 (13.33%) aligned discordantly 1 time ---- 10878330 pairs aligned 0 times concordantly or discordantly; of these: 21756660 mates make up the pairs; of these: 20571124 (94.55%) aligned 0 times 421533 (1.94%) aligned exactly 1 time 764003 (3.51%) aligned >1 times 51.19% overall alignment rate Time searching: 01:06:52 Overall time: 01:06:52 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] 3401166 / 10167868 = 0.3345 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 16:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.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 16:30:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:30:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:30:45: 1000000 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 16:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.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 16:30:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:30:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:31:06: 2000000 INFO @ Tue, 02 Aug 2022 16:31:08: 1000000 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 16:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.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 16:31:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:31:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:31:26: 3000000 INFO @ Tue, 02 Aug 2022 16:31:27: 2000000 INFO @ Tue, 02 Aug 2022 16:31:43: 1000000 INFO @ Tue, 02 Aug 2022 16:31:47: 4000000 INFO @ Tue, 02 Aug 2022 16:31:47: 3000000 INFO @ Tue, 02 Aug 2022 16:32:03: 2000000 INFO @ Tue, 02 Aug 2022 16:32:06: 4000000 INFO @ Tue, 02 Aug 2022 16:32:06: 5000000 INFO @ Tue, 02 Aug 2022 16:32:22: 3000000 INFO @ Tue, 02 Aug 2022 16:32:24: 5000000 INFO @ Tue, 02 Aug 2022 16:32:26: 6000000 INFO @ Tue, 02 Aug 2022 16:32:41: 4000000 INFO @ Tue, 02 Aug 2022 16:32:44: 6000000 INFO @ Tue, 02 Aug 2022 16:32:45: 7000000 INFO @ Tue, 02 Aug 2022 16:32:59: 5000000 INFO @ Tue, 02 Aug 2022 16:33:02: 7000000 INFO @ Tue, 02 Aug 2022 16:33:03: 8000000 INFO @ Tue, 02 Aug 2022 16:33:18: 6000000 INFO @ Tue, 02 Aug 2022 16:33:19: 8000000 INFO @ Tue, 02 Aug 2022 16:33:21: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:33:37: 7000000 INFO @ Tue, 02 Aug 2022 16:33:37: 9000000 INFO @ Tue, 02 Aug 2022 16:33:40: 10000000 INFO @ Tue, 02 Aug 2022 16:33:56: 10000000 INFO @ Tue, 02 Aug 2022 16:33:57: 8000000 INFO @ Tue, 02 Aug 2022 16:33:59: 11000000 INFO @ Tue, 02 Aug 2022 16:34:14: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:34:16: 9000000 INFO @ Tue, 02 Aug 2022 16:34:19: 12000000 INFO @ Tue, 02 Aug 2022 16:34:33: 12000000 INFO @ Tue, 02 Aug 2022 16:34:35: 10000000 INFO @ Tue, 02 Aug 2022 16:34:39: 13000000 INFO @ Tue, 02 Aug 2022 16:34:53: 13000000 INFO @ Tue, 02 Aug 2022 16:34:54: 11000000 INFO @ Tue, 02 Aug 2022 16:34:59: 14000000 INFO @ Tue, 02 Aug 2022 16:35:11: 14000000 INFO @ Tue, 02 Aug 2022 16:35:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:35:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:35:14: #1 total tags in treatment: 5699333 INFO @ Tue, 02 Aug 2022 16:35:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:35:14: #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 16:35:14: #1 tags after filtering in treatment: 5539084 INFO @ Tue, 02 Aug 2022 16:35:14: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:35:14: #1 finished! INFO @ Tue, 02 Aug 2022 16:35:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:35:15: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 16:35:15: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 16:35:15: start model_add_line... INFO @ Tue, 02 Aug 2022 16:35:15: start X-correlation... INFO @ Tue, 02 Aug 2022 16:35:15: 12000000 INFO @ Tue, 02 Aug 2022 16:35:15: end of X-cor INFO @ Tue, 02 Aug 2022 16:35:15: #2 finished! INFO @ Tue, 02 Aug 2022 16:35:15: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 16:35:15: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 16:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05_model.r WARNING @ Tue, 02 Aug 2022 16:35:15: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:35:15: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 16:35:15: #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 16:35:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:35:25: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:35:25: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:35:25: #1 total tags in treatment: 5699333 INFO @ Tue, 02 Aug 2022 16:35:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:35:25: #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 16:35:25: #1 tags after filtering in treatment: 5539084 INFO @ Tue, 02 Aug 2022 16:35:25: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:35:25: #1 finished! INFO @ Tue, 02 Aug 2022 16:35:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:35:26: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 16:35:26: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 16:35:26: start model_add_line... INFO @ Tue, 02 Aug 2022 16:35:26: start X-correlation... INFO @ Tue, 02 Aug 2022 16:35:26: end of X-cor INFO @ Tue, 02 Aug 2022 16:35:26: #2 finished! INFO @ Tue, 02 Aug 2022 16:35:26: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 16:35:26: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 16:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10_model.r WARNING @ Tue, 02 Aug 2022 16:35:26: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:35:26: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 16:35:26: #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 16:35:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:35:35: 13000000 INFO @ Tue, 02 Aug 2022 16:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.05_summits.bed INFO @ Tue, 02 Aug 2022 16:35:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:35:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:35:54: 14000000 INFO @ Tue, 02 Aug 2022 16:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.10_summits.bed INFO @ Tue, 02 Aug 2022 16:35:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (532 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:36:07: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:36:07: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:36:07: #1 total tags in treatment: 5699333 INFO @ Tue, 02 Aug 2022 16:36:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:36:07: #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 16:36:08: #1 tags after filtering in treatment: 5539084 INFO @ Tue, 02 Aug 2022 16:36:08: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:36:08: #1 finished! INFO @ Tue, 02 Aug 2022 16:36:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:36:08: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 16:36:08: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 16:36:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:36:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:36:08: end of X-cor INFO @ Tue, 02 Aug 2022 16:36:08: #2 finished! INFO @ Tue, 02 Aug 2022 16:36:08: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 16:36:08: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 16:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20_model.r WARNING @ Tue, 02 Aug 2022 16:36:08: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:36:08: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 16:36:08: #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 16:36:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:36:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245084/SRX11245084.20_summits.bed INFO @ Tue, 02 Aug 2022 16:36:37: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 132 millis CompletedMACS2peakCalling