[2024-01-24 13:42:56,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:56,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:56,260] [INFO] DQC Reference Directory: /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference
[2024-01-24 13:42:57,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:57,521] [INFO] Task started: Prodigal
[2024-01-24 13:42:57,521] [INFO] Running command: gunzip -c /var/lib/cwl/stg8135683d-77b3-4781-9647-a57794cdd5d7/GCF_011044175.1_ASM1104417v1_genomic.fna.gz | prodigal -d GCF_011044175.1_ASM1104417v1_genomic.fna/cds.fna -a GCF_011044175.1_ASM1104417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:10,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:10,098] [INFO] Task started: HMMsearch
[2024-01-24 13:43:10,099] [INFO] Running command: hmmsearch --tblout GCF_011044175.1_ASM1104417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/reference_markers.hmm GCF_011044175.1_ASM1104417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:10,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:10,372] [INFO] Found 6/6 markers.
[2024-01-24 13:43:10,405] [INFO] Query marker FASTA was written to GCF_011044175.1_ASM1104417v1_genomic.fna/markers.fasta
[2024-01-24 13:43:10,405] [INFO] Task started: Blastn
[2024-01-24 13:43:10,405] [INFO] Running command: blastn -query GCF_011044175.1_ASM1104417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/reference_markers.fasta -out GCF_011044175.1_ASM1104417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:11,057] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:11,061] [INFO] Selected 29 target genomes.
[2024-01-24 13:43:11,062] [INFO] Target genome list was writen to GCF_011044175.1_ASM1104417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:11,077] [INFO] Task started: fastANI
[2024-01-24 13:43:11,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg8135683d-77b3-4781-9647-a57794cdd5d7/GCF_011044175.1_ASM1104417v1_genomic.fna.gz --refList GCF_011044175.1_ASM1104417v1_genomic.fna/target_genomes.txt --output GCF_011044175.1_ASM1104417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:27,483] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:27,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:27,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:27,508] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:27,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:27,508] [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
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.2758	259	1129	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.9746	84	1129	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.7538	171	1129	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.5723	179	1129	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.4933	102	1129	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	77.2673	103	1129	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	77.2575	100	1129	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.1678	200	1129	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.1619	201	1129	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.126	152	1129	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	77.1241	95	1129	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	77.0628	153	1129	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	77.0566	96	1129	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.0127	120	1129	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	76.9828	118	1129	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.9432	181	1129	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.7862	70	1129	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.7685	84	1129	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.7518	86	1129	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.6798	70	1129	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.6684	90	1129	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.6663	89	1129	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.638	60	1129	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.6278	119	1129	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.5987	87	1129	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.3537	89	1129	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.3331	79	1129	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	76.2826	78	1129	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.9015	70	1129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:27,510] [INFO] DFAST Taxonomy check result was written to GCF_011044175.1_ASM1104417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:27,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:27,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:27,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/checkm_data
[2024-01-24 13:43:27,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:27,551] [INFO] Task started: CheckM
[2024-01-24 13:43:27,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044175.1_ASM1104417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044175.1_ASM1104417v1_genomic.fna/checkm_input GCF_011044175.1_ASM1104417v1_genomic.fna/checkm_result
[2024-01-24 13:44:06,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:06,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:06,707] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:06,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:06,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044175.1_ASM1104417v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:06,708] [INFO] Task started: Blastn
[2024-01-24 13:44:06,708] [INFO] Running command: blastn -query GCF_011044175.1_ASM1104417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge13f255b-4475-4804-8475-7e3f16c2813e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044175.1_ASM1104417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:07,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:07,563] [INFO] Selected 16 target genomes.
[2024-01-24 13:44:07,563] [INFO] Target genome list was writen to GCF_011044175.1_ASM1104417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:07,590] [INFO] Task started: fastANI
[2024-01-24 13:44:07,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg8135683d-77b3-4781-9647-a57794cdd5d7/GCF_011044175.1_ASM1104417v1_genomic.fna.gz --refList GCF_011044175.1_ASM1104417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044175.1_ASM1104417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:17,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:17,119] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:17,120] [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_011044175.1	s__Marinirhabdus sp011044175	100.0	1129	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002375495.1	s__Marinirhabdus sp002375495	78.6858	427	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.261	260	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	78.1802	364	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCA_002707745.1	s__Marinirhabdus sp002707745	78.1763	260	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.7236	174	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.5794	180	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000170815.1	s__Patiriisocius sp000170815	77.2883	164	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	77.2416	102	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102055.1	s__Ulvibacter litoralis	77.1806	200	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	77.1739	75	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.126	152	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	77.0745	94	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_006346335.1	s__Aequorivita sinensis	76.9912	121	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.7518	86	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.4065	90	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:17,121] [INFO] GTDB search result was written to GCF_011044175.1_ASM1104417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:17,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:17,127] [INFO] DFAST_QC result json was written to GCF_011044175.1_ASM1104417v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:17,127] [INFO] DFAST_QC completed!
[2024-01-24 13:44:17,127] [INFO] Total running time: 0h1m21s