[2024-01-24 13:19:25,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference
[2024-01-24 13:19:26,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,792] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,792] [INFO] Running command: gunzip -c /var/lib/cwl/stge5fbebab-c45d-4dc4-92fc-f7399d48f2a9/GCF_031451685.1_ASM3145168v1_genomic.fna.gz | prodigal -d GCF_031451685.1_ASM3145168v1_genomic.fna/cds.fna -a GCF_031451685.1_ASM3145168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:37,007] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:37,007] [INFO] Task started: HMMsearch
[2024-01-24 13:19:37,007] [INFO] Running command: hmmsearch --tblout GCF_031451685.1_ASM3145168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/reference_markers.hmm GCF_031451685.1_ASM3145168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:37,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:37,229] [INFO] Found 6/6 markers.
[2024-01-24 13:19:37,260] [INFO] Query marker FASTA was written to GCF_031451685.1_ASM3145168v1_genomic.fna/markers.fasta
[2024-01-24 13:19:37,261] [INFO] Task started: Blastn
[2024-01-24 13:19:37,261] [INFO] Running command: blastn -query GCF_031451685.1_ASM3145168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/reference_markers.fasta -out GCF_031451685.1_ASM3145168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:38,161] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:38,164] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:38,165] [INFO] Target genome list was writen to GCF_031451685.1_ASM3145168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:38,174] [INFO] Task started: fastANI
[2024-01-24 13:19:38,175] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fbebab-c45d-4dc4-92fc-f7399d48f2a9/GCF_031451685.1_ASM3145168v1_genomic.fna.gz --refList GCF_031451685.1_ASM3145168v1_genomic.fna/target_genomes.txt --output GCF_031451685.1_ASM3145168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:58,218] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:58,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:58,235] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:58,235] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:58,235] [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 campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	88.21	887	1156	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	86.6665	824	1156	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	85.9069	784	1156	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.0546	779	1156	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	84.8623	821	1156	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	84.8239	807	1156	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	84.8103	832	1156	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	83.5205	760	1156	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	83.3233	732	1156	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	83.2525	726	1156	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.1369	749	1156	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.0451	727	1156	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	82.935	737	1156	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.7851	746	1156	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	82.5385	747	1156	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	82.358	722	1156	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.2465	720	1156	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	80.2796	532	1156	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	78.0335	419	1156	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	77.4723	254	1156	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	77.3207	295	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,237] [INFO] DFAST Taxonomy check result was written to GCF_031451685.1_ASM3145168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:58,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:58,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:58,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/checkm_data
[2024-01-24 13:19:58,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:58,276] [INFO] Task started: CheckM
[2024-01-24 13:19:58,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451685.1_ASM3145168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451685.1_ASM3145168v1_genomic.fna/checkm_input GCF_031451685.1_ASM3145168v1_genomic.fna/checkm_result
[2024-01-24 13:20:30,165] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:30,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:30,186] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:30,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:30,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451685.1_ASM3145168v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:30,187] [INFO] Task started: Blastn
[2024-01-24 13:20:30,187] [INFO] Running command: blastn -query GCF_031451685.1_ASM3145168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f88deb-e68c-4c59-82a0-03f5feb957ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451685.1_ASM3145168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:31,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:31,768] [INFO] Selected 18 target genomes.
[2024-01-24 13:20:31,768] [INFO] Target genome list was writen to GCF_031451685.1_ASM3145168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:31,786] [INFO] Task started: fastANI
[2024-01-24 13:20:31,786] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fbebab-c45d-4dc4-92fc-f7399d48f2a9/GCF_031451685.1_ASM3145168v1_genomic.fna.gz --refList GCF_031451685.1_ASM3145168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451685.1_ASM3145168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:46,032] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:46,047] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:46,047] [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_003182195.1	s__Halomonas sp003182195	90.1511	838	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCA_003552795.1	s__Halomonas sp003552795	88.6835	644	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	88.352	754	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	88.2117	887	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560175.1	s__Halomonas sp003560175	86.8091	523	1156	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	86.6893	822	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_009902005.1	s__Halomonas alimentaria	85.912	784	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	85.7178	738	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	84.8313	806	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003202205.1	s__Halomonas sp003202205	84.7906	793	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	83.5386	758	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361885.1	s__Halomonas ventosae_C	83.2748	645	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620045.1	s__Halomonas halodenitrificans	83.2585	726	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.15	97.15	0.89	0.89	2	-
GCF_014192215.1	s__Halomonas cerina	82.9503	736	1156	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	82.6078	711	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286975.1	s__Halomonas_B sp002286975	82.5316	747	1156	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	81.8256	675	1156	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_002374315.1	s__Halomonas nigrificans	79.9706	141	1156	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 13:20:46,049] [INFO] GTDB search result was written to GCF_031451685.1_ASM3145168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:46,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:46,054] [INFO] DFAST_QC result json was written to GCF_031451685.1_ASM3145168v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:46,054] [INFO] DFAST_QC completed!
[2024-01-24 13:20:46,054] [INFO] Total running time: 0h1m21s