[2023-03-18 01:59:39,745] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference
[2023-03-18 01:59:40,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,968] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,969] [INFO] Running command: cat /var/lib/cwl/stg56c93f15-2e00-4359-908c-ebde61756cee/OceanDNA-b30950.fa | prodigal -d OceanDNA-b30950/cds.fna -a OceanDNA-b30950/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:59,890] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:59,891] [INFO] Task started: HMMsearch
[2023-03-18 01:59:59,891] [INFO] Running command: hmmsearch --tblout OceanDNA-b30950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/reference_markers.hmm OceanDNA-b30950/protein.faa > /dev/null
[2023-03-18 02:00:00,104] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:00:00,105] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg56c93f15-2e00-4359-908c-ebde61756cee/OceanDNA-b30950.fa]
[2023-03-18 02:00:00,140] [INFO] Query marker FASTA was written to OceanDNA-b30950/markers.fasta
[2023-03-18 02:00:00,140] [INFO] Task started: Blastn
[2023-03-18 02:00:00,140] [INFO] Running command: blastn -query OceanDNA-b30950/markers.fasta -db /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/reference_markers.fasta -out OceanDNA-b30950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:00,895] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:00,912] [INFO] Selected 24 target genomes.
[2023-03-18 02:00:00,913] [INFO] Target genome list was writen to OceanDNA-b30950/target_genomes.txt
[2023-03-18 02:00:00,929] [INFO] Task started: fastANI
[2023-03-18 02:00:00,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c93f15-2e00-4359-908c-ebde61756cee/OceanDNA-b30950.fa --refList OceanDNA-b30950/target_genomes.txt --output OceanDNA-b30950/fastani_result.tsv --threads 1
[2023-03-18 02:00:18,068] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:18,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:18,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:18,081] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:18,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:00:18,081] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.2649	133	1025	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.1763	91	1025	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.1681	112	1025	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.1595	87	1025	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1595	87	1025	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.1097	120	1025	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.0727	88	1025	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	75.9487	68	1025	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.9422	110	1025	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.9373	116	1025	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.9145	114	1025	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.8798	113	1025	95	below_threshold
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	75.8548	52	1025	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.6865	76	1025	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.6733	75	1025	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	75.6222	62	1025	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.5412	128	1025	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.4392	60	1025	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.3811	53	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:00:18,082] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30950/tc_result.tsv
[2023-03-18 02:00:18,084] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:18,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:18,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/checkm_data
[2023-03-18 02:00:18,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:18,163] [INFO] Task started: CheckM
[2023-03-18 02:00:18,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30950/checkm_input OceanDNA-b30950/checkm_result
[2023-03-18 02:01:06,513] [INFO] Task succeeded: CheckM
[2023-03-18 02:01:06,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:01:06,568] [INFO] ===== Completeness check finished =====
[2023-03-18 02:01:06,569] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:01:06,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30950/markers.fasta)
[2023-03-18 02:01:06,570] [INFO] Task started: Blastn
[2023-03-18 02:01:06,570] [INFO] Running command: blastn -query OceanDNA-b30950/markers.fasta -db /var/lib/cwl/stg0127859f-6923-4fa2-80ac-92e39a835b39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:01:08,005] [INFO] Task succeeded: Blastn
[2023-03-18 02:01:08,010] [INFO] Selected 14 target genomes.
[2023-03-18 02:01:08,010] [INFO] Target genome list was writen to OceanDNA-b30950/target_genomes_gtdb.txt
[2023-03-18 02:01:08,027] [INFO] Task started: fastANI
[2023-03-18 02:01:08,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg56c93f15-2e00-4359-908c-ebde61756cee/OceanDNA-b30950.fa --refList OceanDNA-b30950/target_genomes_gtdb.txt --output OceanDNA-b30950/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:01:18,305] [INFO] Task succeeded: fastANI
[2023-03-18 02:01:18,314] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:01:18,314] [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	80.9031	691	1025	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_002696205.1	s__UBA1479 sp002696205	80.755	558	1025	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_002706405.1	s__UBA1479 sp002706405	80.4178	605	1025	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	80.3825	597	1025	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	79.9458	531	1025	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_014382345.1	s__Casp-alpha2 sp014382345	76.4875	139	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.442	119	1025	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_016776525.1	s__JADHTD01 sp016776525	76.3937	78	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	76.3772	67	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.2649	133	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195125.1	s__Phaeospirillum sp016195125	75.6905	87	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344765.1	s__Ferruginivarius sediminum	75.6865	76	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	75.5497	127	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_000802185.1	s__Belnapia sp000802185	75.1856	65	1025	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:01:18,316] [INFO] GTDB search result was written to OceanDNA-b30950/result_gtdb.tsv
[2023-03-18 02:01:18,318] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:01:18,322] [INFO] DFAST_QC result json was written to OceanDNA-b30950/dqc_result.json
[2023-03-18 02:01:18,322] [INFO] DFAST_QC completed!
[2023-03-18 02:01:18,322] [INFO] Total running time: 0h1m39s