Job ID = 12264762 SRX = SRX3029127 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27055709 spots for SRR5860427/SRR5860427.sra Written 27055709 spots for SRR5860427/SRR5860427.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265367 ("srTce11") 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: 00:24:59 27055709 reads; of these: 27055709 (100.00%) were paired; of these: 12347711 (45.64%) aligned concordantly 0 times 12680797 (46.87%) aligned concordantly exactly 1 time 2027201 (7.49%) aligned concordantly >1 times ---- 12347711 pairs aligned concordantly 0 times; of these: 2154781 (17.45%) aligned discordantly 1 time ---- 10192930 pairs aligned 0 times concordantly or discordantly; of these: 20385860 mates make up the pairs; of these: 19298725 (94.67%) aligned 0 times 461826 (2.27%) aligned exactly 1 time 625309 (3.07%) aligned >1 times 64.34% overall alignment rate Time searching: 00:24:59 Overall time: 00:24:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 4976800 / 16688622 = 0.2982 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 06:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:36:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:36:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:36:20: 1000000 INFO @ Sat, 03 Apr 2021 06:36:28: 2000000 INFO @ Sat, 03 Apr 2021 06:36:35: 3000000 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 06:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:36:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:36:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:36:43: 4000000 INFO @ Sat, 03 Apr 2021 06:36:49: 1000000 INFO @ Sat, 03 Apr 2021 06:36:50: 5000000 INFO @ Sat, 03 Apr 2021 06:36:56: 2000000 INFO @ Sat, 03 Apr 2021 06:36:58: 6000000 INFO @ Sat, 03 Apr 2021 06:37:03: 3000000 INFO @ Sat, 03 Apr 2021 06:37:06: 7000000 INFO @ Sat, 03 Apr 2021 06:37:09: 4000000 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 06:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:37:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:37:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:37:13: 8000000 INFO @ Sat, 03 Apr 2021 06:37:16: 5000000 INFO @ Sat, 03 Apr 2021 06:37:21: 1000000 INFO @ Sat, 03 Apr 2021 06:37:21: 9000000 INFO @ Sat, 03 Apr 2021 06:37:23: 6000000 INFO @ Sat, 03 Apr 2021 06:37:30: 10000000 INFO @ Sat, 03 Apr 2021 06:37:30: 7000000 INFO @ Sat, 03 Apr 2021 06:37:31: 2000000 INFO @ Sat, 03 Apr 2021 06:37:37: 8000000 INFO @ Sat, 03 Apr 2021 06:37:38: 11000000 INFO @ Sat, 03 Apr 2021 06:37:41: 3000000 INFO @ Sat, 03 Apr 2021 06:37:45: 9000000 INFO @ Sat, 03 Apr 2021 06:37:45: 12000000 INFO @ Sat, 03 Apr 2021 06:37:48: 4000000 INFO @ Sat, 03 Apr 2021 06:37:53: 13000000 INFO @ Sat, 03 Apr 2021 06:37:53: 10000000 INFO @ Sat, 03 Apr 2021 06:37:56: 5000000 INFO @ Sat, 03 Apr 2021 06:38:01: 11000000 INFO @ Sat, 03 Apr 2021 06:38:01: 14000000 INFO @ Sat, 03 Apr 2021 06:38:03: 6000000 INFO @ Sat, 03 Apr 2021 06:38:08: 12000000 INFO @ Sat, 03 Apr 2021 06:38:09: 15000000 INFO @ Sat, 03 Apr 2021 06:38:10: 7000000 INFO @ Sat, 03 Apr 2021 06:38:15: 13000000 INFO @ Sat, 03 Apr 2021 06:38:16: 16000000 INFO @ Sat, 03 Apr 2021 06:38:21: 8000000 INFO @ Sat, 03 Apr 2021 06:38:21: 14000000 INFO @ Sat, 03 Apr 2021 06:38:25: 17000000 INFO @ Sat, 03 Apr 2021 06:38:28: 15000000 INFO @ Sat, 03 Apr 2021 06:38:31: 9000000 INFO @ Sat, 03 Apr 2021 06:38:32: 18000000 INFO @ Sat, 03 Apr 2021 06:38:35: 16000000 INFO @ Sat, 03 Apr 2021 06:38:40: 19000000 INFO @ Sat, 03 Apr 2021 06:38:41: 10000000 INFO @ Sat, 03 Apr 2021 06:38:43: 17000000 INFO @ Sat, 03 Apr 2021 06:38:49: 20000000 INFO @ Sat, 03 Apr 2021 06:38:50: 18000000 INFO @ Sat, 03 Apr 2021 06:38:51: 11000000 INFO @ Sat, 03 Apr 2021 06:38:57: 19000000 INFO @ Sat, 03 Apr 2021 06:38:58: 21000000 INFO @ Sat, 03 Apr 2021 06:39:01: 12000000 INFO @ Sat, 03 Apr 2021 06:39:04: 20000000 INFO @ Sat, 03 Apr 2021 06:39:08: 22000000 INFO @ Sat, 03 Apr 2021 06:39:10: 13000000 INFO @ Sat, 03 Apr 2021 06:39:12: 21000000 INFO @ Sat, 03 Apr 2021 06:39:16: 23000000 INFO @ Sat, 03 Apr 2021 06:39:19: 22000000 INFO @ Sat, 03 Apr 2021 06:39:20: 14000000 INFO @ Sat, 03 Apr 2021 06:39:24: 24000000 INFO @ Sat, 03 Apr 2021 06:39:26: 23000000 INFO @ Sat, 03 Apr 2021 06:39:27: 15000000 INFO @ Sat, 03 Apr 2021 06:39:30: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:39:30: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:39:30: #1 total tags in treatment: 10376844 INFO @ Sat, 03 Apr 2021 06:39:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:39:30: #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 06:39:30: #1 tags after filtering in treatment: 7632500 INFO @ Sat, 03 Apr 2021 06:39:30: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:39:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:39:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:39:31: #2 number of paired peaks: 681 WARNING @ Sat, 03 Apr 2021 06:39:31: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Sat, 03 Apr 2021 06:39:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:39:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:39:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:39:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:39:31: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 06:39:31: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 06:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05_model.r WARNING @ Sat, 03 Apr 2021 06:39:31: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:39:31: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 06:39:31: #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 06:39:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:39:34: 24000000 INFO @ Sat, 03 Apr 2021 06:39:34: 16000000 INFO @ Sat, 03 Apr 2021 06:39:39: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:39:39: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:39:39: #1 total tags in treatment: 10376844 INFO @ Sat, 03 Apr 2021 06:39:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:39:39: #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 06:39:40: #1 tags after filtering in treatment: 7632500 INFO @ Sat, 03 Apr 2021 06:39:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:39:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:39:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:39:40: #2 number of paired peaks: 681 WARNING @ Sat, 03 Apr 2021 06:39:40: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Sat, 03 Apr 2021 06:39:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:39:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:39:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:39:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:39:40: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 06:39:40: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 06:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10_model.r WARNING @ Sat, 03 Apr 2021 06:39:40: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:39:40: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 06:39:40: #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 06:39:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:39:40: 17000000 INFO @ Sat, 03 Apr 2021 06:39:47: 18000000 INFO @ Sat, 03 Apr 2021 06:39:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:39:53: 19000000 INFO @ Sat, 03 Apr 2021 06:39:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.05_summits.bed INFO @ Sat, 03 Apr 2021 06:39:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5976 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:40:00: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.10_summits.bed INFO @ Sat, 03 Apr 2021 06:40:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3503 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:40:06: 21000000 INFO @ Sat, 03 Apr 2021 06:40:12: 22000000 INFO @ Sat, 03 Apr 2021 06:40:19: 23000000 INFO @ Sat, 03 Apr 2021 06:40:26: 24000000 INFO @ Sat, 03 Apr 2021 06:40:30: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:40:30: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:40:30: #1 total tags in treatment: 10376844 INFO @ Sat, 03 Apr 2021 06:40:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:40:30: #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 06:40:31: #1 tags after filtering in treatment: 7632500 INFO @ Sat, 03 Apr 2021 06:40:31: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:40:31: #1 finished! INFO @ Sat, 03 Apr 2021 06:40:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:40:31: #2 number of paired peaks: 681 WARNING @ Sat, 03 Apr 2021 06:40:31: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Sat, 03 Apr 2021 06:40:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:40:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:40:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:40:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:40:31: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 06:40:31: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 06:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20_model.r WARNING @ Sat, 03 Apr 2021 06:40:31: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:40:31: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 06:40:31: #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 06:40:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:40:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029127/SRX3029127.20_summits.bed INFO @ Sat, 03 Apr 2021 06:40:55: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (1600 records, 4 fields): 5 millis CompletedMACS2peakCalling