[2023-03-14 11:40:05,552] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,553] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference
[2023-03-14 11:40:06,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,687] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,687] [INFO] Running command: cat /var/lib/cwl/stg73534f5e-cd60-4b59-a158-01c774a85d0d/OceanDNA-b30960.fa | prodigal -d OceanDNA-b30960/cds.fna -a OceanDNA-b30960/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:26,234] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:26,234] [INFO] Task started: HMMsearch
[2023-03-14 11:40:26,234] [INFO] Running command: hmmsearch --tblout OceanDNA-b30960/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/reference_markers.hmm OceanDNA-b30960/protein.faa > /dev/null
[2023-03-14 11:40:26,433] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:26,433] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg73534f5e-cd60-4b59-a158-01c774a85d0d/OceanDNA-b30960.fa]
[2023-03-14 11:40:26,466] [INFO] Query marker FASTA was written to OceanDNA-b30960/markers.fasta
[2023-03-14 11:40:26,467] [INFO] Task started: Blastn
[2023-03-14 11:40:26,467] [INFO] Running command: blastn -query OceanDNA-b30960/markers.fasta -db /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/reference_markers.fasta -out OceanDNA-b30960/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:27,269] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:27,273] [INFO] Selected 26 target genomes.
[2023-03-14 11:40:27,274] [INFO] Target genome list was writen to OceanDNA-b30960/target_genomes.txt
[2023-03-14 11:40:27,289] [INFO] Task started: fastANI
[2023-03-14 11:40:27,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg73534f5e-cd60-4b59-a158-01c774a85d0d/OceanDNA-b30960.fa --refList OceanDNA-b30960/target_genomes.txt --output OceanDNA-b30960/fastani_result.tsv --threads 1
[2023-03-14 11:40:48,916] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:48,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:48,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:48,931] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:48,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:40:48,931] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8096	166	1051	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.7072	169	1051	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.6656	171	1051	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.6261	176	1051	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.6071	140	1051	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.5164	178	1051	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4837	207	1051	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.4579	224	1051	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.449	158	1051	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4354	218	1051	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.408	149	1051	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.4036	155	1051	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.3769	191	1051	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.2933	207	1051	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.2806	154	1051	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.2786	212	1051	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.2603	205	1051	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.2275	202	1051	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2085	216	1051	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.1178	132	1051	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.8723	100	1051	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.7383	98	1051	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.6715	120	1051	95	below_threshold
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	75.6452	59	1051	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.5442	106	1051	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.5032	126	1051	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:40:48,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30960/tc_result.tsv
[2023-03-14 11:40:48,938] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:48,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:48,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/checkm_data
[2023-03-14 11:40:48,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:48,946] [INFO] Task started: CheckM
[2023-03-14 11:40:48,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30960/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30960/checkm_input OceanDNA-b30960/checkm_result
[2023-03-14 11:41:38,135] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:38,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:38,147] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:38,147] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:38,147] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30960/markers.fasta)
[2023-03-14 11:41:38,147] [INFO] Task started: Blastn
[2023-03-14 11:41:38,147] [INFO] Running command: blastn -query OceanDNA-b30960/markers.fasta -db /var/lib/cwl/stgb5334ab8-5b2f-4736-8b6a-c640f3d7c122/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30960/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:39,635] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:39,641] [INFO] Selected 11 target genomes.
[2023-03-14 11:41:39,641] [INFO] Target genome list was writen to OceanDNA-b30960/target_genomes_gtdb.txt
[2023-03-14 11:41:39,649] [INFO] Task started: fastANI
[2023-03-14 11:41:39,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg73534f5e-cd60-4b59-a158-01c774a85d0d/OceanDNA-b30960.fa --refList OceanDNA-b30960/target_genomes_gtdb.txt --output OceanDNA-b30960/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:47,264] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:47,271] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:47,271] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002325375.1	s__UBA1479 sp002325375	90.1847	933	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002706405.1	s__UBA1479 sp002706405	88.1381	769	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002781745.1	s__UBA1479 sp002781745	84.6741	738	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696205.1	s__UBA1479 sp002696205	83.1782	661	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433335.1	s__UBA1479 sp002433335	81.3933	655	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.4796	187	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.8827	189	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	76.4172	154	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.4161	159	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.2192	136	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380005.1	s__Magnetospirillum sp014380005	76.1521	127	1051	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:47,274] [INFO] GTDB search result was written to OceanDNA-b30960/result_gtdb.tsv
[2023-03-14 11:41:47,277] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:47,282] [INFO] DFAST_QC result json was written to OceanDNA-b30960/dqc_result.json
[2023-03-14 11:41:47,282] [INFO] DFAST_QC completed!
[2023-03-14 11:41:47,282] [INFO] Total running time: 0h1m42s