[2023-06-19 05:51:57,530] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:57,536] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:57,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference
[2023-06-19 05:52:00,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:52:00,298] [INFO] Task started: Prodigal
[2023-06-19 05:52:00,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg2450175c-931d-436d-b6e2-cdb3a25c3082/GCA_013203955.1_ASM1320395v1_genomic.fna.gz | prodigal -d GCA_013203955.1_ASM1320395v1_genomic.fna/cds.fna -a GCA_013203955.1_ASM1320395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:52:08,626] [INFO] Task succeeded: Prodigal
[2023-06-19 05:52:08,627] [INFO] Task started: HMMsearch
[2023-06-19 05:52:08,627] [INFO] Running command: hmmsearch --tblout GCA_013203955.1_ASM1320395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/reference_markers.hmm GCA_013203955.1_ASM1320395v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:52:08,889] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:52:08,890] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2450175c-931d-436d-b6e2-cdb3a25c3082/GCA_013203955.1_ASM1320395v1_genomic.fna.gz]
[2023-06-19 05:52:08,926] [INFO] Query marker FASTA was written to GCA_013203955.1_ASM1320395v1_genomic.fna/markers.fasta
[2023-06-19 05:52:08,927] [INFO] Task started: Blastn
[2023-06-19 05:52:08,927] [INFO] Running command: blastn -query GCA_013203955.1_ASM1320395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/reference_markers.fasta -out GCA_013203955.1_ASM1320395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:09,616] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:09,621] [INFO] Selected 33 target genomes.
[2023-06-19 05:52:09,621] [INFO] Target genome list was writen to GCA_013203955.1_ASM1320395v1_genomic.fna/target_genomes.txt
[2023-06-19 05:52:09,626] [INFO] Task started: fastANI
[2023-06-19 05:52:09,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg2450175c-931d-436d-b6e2-cdb3a25c3082/GCA_013203955.1_ASM1320395v1_genomic.fna.gz --refList GCA_013203955.1_ASM1320395v1_genomic.fna/target_genomes.txt --output GCA_013203955.1_ASM1320395v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:52:33,903] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:33,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:52:33,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:52:33,930] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:52:33,930] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:52:33,931] [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 gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.0163	75	918	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.9925	83	918	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.6499	64	918	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.5816	93	918	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.4836	82	918	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.4725	88	918	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.4239	61	918	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.4101	79	918	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.3867	71	918	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.3325	70	918	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.3156	88	918	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.2919	72	918	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.2301	66	918	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.1694	56	918	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.1638	56	918	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.1558	83	918	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	75.1193	62	918	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	75.0232	52	918	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:52:33,935] [INFO] DFAST Taxonomy check result was written to GCA_013203955.1_ASM1320395v1_genomic.fna/tc_result.tsv
[2023-06-19 05:52:33,936] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:52:33,936] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:52:33,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/checkm_data
[2023-06-19 05:52:33,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:52:33,978] [INFO] Task started: CheckM
[2023-06-19 05:52:33,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013203955.1_ASM1320395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013203955.1_ASM1320395v1_genomic.fna/checkm_input GCA_013203955.1_ASM1320395v1_genomic.fna/checkm_result
[2023-06-19 05:53:03,631] [INFO] Task succeeded: CheckM
[2023-06-19 05:53:03,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-19 05:53:03,670] [INFO] ===== Completeness check finished =====
[2023-06-19 05:53:03,671] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:53:03,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013203955.1_ASM1320395v1_genomic.fna/markers.fasta)
[2023-06-19 05:53:03,672] [INFO] Task started: Blastn
[2023-06-19 05:53:03,672] [INFO] Running command: blastn -query GCA_013203955.1_ASM1320395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca71804f-dc6f-4097-b9dd-ede186494d48/dqc_reference/reference_markers_gtdb.fasta -out GCA_013203955.1_ASM1320395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:53:04,732] [INFO] Task succeeded: Blastn
[2023-06-19 05:53:04,738] [INFO] Selected 13 target genomes.
[2023-06-19 05:53:04,738] [INFO] Target genome list was writen to GCA_013203955.1_ASM1320395v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:53:04,744] [INFO] Task started: fastANI
[2023-06-19 05:53:04,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg2450175c-931d-436d-b6e2-cdb3a25c3082/GCA_013203955.1_ASM1320395v1_genomic.fna.gz --refList GCA_013203955.1_ASM1320395v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013203955.1_ASM1320395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:53:10,819] [INFO] Task succeeded: fastANI
[2023-06-19 05:53:10,831] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:53:10,832] [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_013203955.1	s__Casp-alpha2 sp013203955	100.0	910	918	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	conclusive
GCA_001510075.1	s__Casp-alpha2 sp001510075	79.2719	297	918	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	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	79.1551	377	918	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_002938075.1	s__Casp-alpha2 sp002938075	78.6806	275	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	78.1938	348	918	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_016763915.1	s__Casp-alpha2 sp016763915	78.1217	180	918	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	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	77.801	273	918	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	-
GCA_002938315.1	s__Casp-alpha2 sp002938315	77.6915	264	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_002325375.1	s__UBA1479 sp002325375	76.5386	142	918	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_009693905.1	s__2-12-FULL-67-15 sp009693905	75.956	74	918	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:53:10,834] [INFO] GTDB search result was written to GCA_013203955.1_ASM1320395v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:53:10,834] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:53:10,840] [INFO] DFAST_QC result json was written to GCA_013203955.1_ASM1320395v1_genomic.fna/dqc_result.json
[2023-06-19 05:53:10,841] [INFO] DFAST_QC completed!
[2023-06-19 05:53:10,841] [INFO] Total running time: 0h1m13s