[2024-01-24 13:01:19,203] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference
[2024-01-24 13:01:20,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,537] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea461bc-dbdb-4a83-bfec-1ce93c4dfeef/GCF_031451695.1_ASM3145169v1_genomic.fna.gz | prodigal -d GCF_031451695.1_ASM3145169v1_genomic.fna/cds.fna -a GCF_031451695.1_ASM3145169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:34,031] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:34,032] [INFO] Task started: HMMsearch
[2024-01-24 13:01:34,032] [INFO] Running command: hmmsearch --tblout GCF_031451695.1_ASM3145169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/reference_markers.hmm GCF_031451695.1_ASM3145169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,337] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,390] [INFO] Query marker FASTA was written to GCF_031451695.1_ASM3145169v1_genomic.fna/markers.fasta
[2024-01-24 13:01:34,391] [INFO] Task started: Blastn
[2024-01-24 13:01:34,391] [INFO] Running command: blastn -query GCF_031451695.1_ASM3145169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/reference_markers.fasta -out GCF_031451695.1_ASM3145169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:35,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:35,321] [INFO] Selected 25 target genomes.
[2024-01-24 13:01:35,321] [INFO] Target genome list was writen to GCF_031451695.1_ASM3145169v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:35,373] [INFO] Task started: fastANI
[2024-01-24 13:01:35,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea461bc-dbdb-4a83-bfec-1ce93c4dfeef/GCF_031451695.1_ASM3145169v1_genomic.fna.gz --refList GCF_031451695.1_ASM3145169v1_genomic.fna/target_genomes.txt --output GCF_031451695.1_ASM3145169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:58,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:58,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:58,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:58,064] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:58,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:58,064] [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
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	93.784	1276	1523	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	88.8445	1154	1523	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.2441	856	1523	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.9756	768	1523	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	82.8878	803	1523	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	82.7597	875	1523	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	82.6732	754	1523	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.649	839	1523	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	82.6109	727	1523	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.5737	696	1523	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	82.4547	769	1523	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	82.4337	880	1523	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.4049	840	1523	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	82.4002	726	1523	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	82.2542	678	1523	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	82.0946	826	1523	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	81.897	824	1523	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.8611	846	1523	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	81.7115	803	1523	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	81.5559	772	1523	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.2445	714	1523	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	79.5683	553	1523	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.2155	385	1523	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.1611	413	1523	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	76.64	170	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:58,066] [INFO] DFAST Taxonomy check result was written to GCF_031451695.1_ASM3145169v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:58,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:58,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:58,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/checkm_data
[2024-01-24 13:01:58,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:58,116] [INFO] Task started: CheckM
[2024-01-24 13:01:58,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451695.1_ASM3145169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451695.1_ASM3145169v1_genomic.fna/checkm_input GCF_031451695.1_ASM3145169v1_genomic.fna/checkm_result
[2024-01-24 13:02:39,214] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:39,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:39,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:39,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:39,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451695.1_ASM3145169v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:39,239] [INFO] Task started: Blastn
[2024-01-24 13:02:39,240] [INFO] Running command: blastn -query GCF_031451695.1_ASM3145169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41d5476a-4625-4e88-b0a3-a0a00e94f175/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451695.1_ASM3145169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:40,691] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:40,695] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:40,695] [INFO] Target genome list was writen to GCF_031451695.1_ASM3145169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:40,710] [INFO] Task started: fastANI
[2024-01-24 13:02:40,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea461bc-dbdb-4a83-bfec-1ce93c4dfeef/GCF_031451695.1_ASM3145169v1_genomic.fna.gz --refList GCF_031451695.1_ASM3145169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451695.1_ASM3145169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:53,694] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:53,707] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:02:53,707] [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
GCF_002286975.1	s__Halomonas_B sp002286975	93.7809	1277	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	92.5538	1205	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	92.2814	1149	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	88.8569	1152	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	87.749	1191	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	82.9085	685	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	82.6559	755	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_010994375.1	s__Halomonas sp010994375	82.2568	795	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	81.9283	820	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	81.5993	750	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	81.5085	691	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374315.1	s__Halomonas nigrificans	79.0262	182	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:53,709] [INFO] GTDB search result was written to GCF_031451695.1_ASM3145169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:53,709] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:53,713] [INFO] DFAST_QC result json was written to GCF_031451695.1_ASM3145169v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:53,713] [INFO] DFAST_QC completed!
[2024-01-24 13:02:53,714] [INFO] Total running time: 0h1m35s