[2024-01-24 10:58:06,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,471] [INFO] DQC Reference Directory: /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f004cf3-3fb2-4840-a026-8825b1191a25/GCF_012062845.1_ASM1206284v1_genomic.fna.gz | prodigal -d GCF_012062845.1_ASM1206284v1_genomic.fna/cds.fna -a GCF_012062845.1_ASM1206284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:19,552] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:19,553] [INFO] Task started: HMMsearch
[2024-01-24 10:58:19,553] [INFO] Running command: hmmsearch --tblout GCF_012062845.1_ASM1206284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/reference_markers.hmm GCF_012062845.1_ASM1206284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:19,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:19,873] [INFO] Found 6/6 markers.
[2024-01-24 10:58:19,904] [INFO] Query marker FASTA was written to GCF_012062845.1_ASM1206284v1_genomic.fna/markers.fasta
[2024-01-24 10:58:19,905] [INFO] Task started: Blastn
[2024-01-24 10:58:19,905] [INFO] Running command: blastn -query GCF_012062845.1_ASM1206284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/reference_markers.fasta -out GCF_012062845.1_ASM1206284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:20,839] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:20,843] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:20,844] [INFO] Target genome list was writen to GCF_012062845.1_ASM1206284v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:20,852] [INFO] Task started: fastANI
[2024-01-24 10:58:20,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f004cf3-3fb2-4840-a026-8825b1191a25/GCF_012062845.1_ASM1206284v1_genomic.fna.gz --refList GCF_012062845.1_ASM1206284v1_genomic.fna/target_genomes.txt --output GCF_012062845.1_ASM1206284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:34,267] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:34,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:34,292] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:34,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:34,292] [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 niordiana	strain=ATF 5.4	GCA_004798965.1	2508711	2508711	type	True	93.4392	933	1108	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	84.2149	787	1108	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	80.9626	527	1108	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	80.8699	599	1108	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	80.7883	567	1108	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.0763	534	1108	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	80.0655	568	1108	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	80.0205	506	1108	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.9551	512	1108	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	79.9004	469	1108	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.8005	505	1108	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	79.674	467	1108	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	79.6507	473	1108	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.6112	471	1108	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.5677	466	1108	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	79.395	433	1108	95	below_threshold
Halomonas qijiaojingensis	strain=KCTC 22228	GCA_014651875.1	980347	980347	type	True	79.0713	481	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,294] [INFO] DFAST Taxonomy check result was written to GCF_012062845.1_ASM1206284v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:34,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:34,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:34,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/checkm_data
[2024-01-24 10:58:34,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:34,333] [INFO] Task started: CheckM
[2024-01-24 10:58:34,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012062845.1_ASM1206284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012062845.1_ASM1206284v1_genomic.fna/checkm_input GCF_012062845.1_ASM1206284v1_genomic.fna/checkm_result
[2024-01-24 10:59:08,290] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:08,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,316] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:08,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:08,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012062845.1_ASM1206284v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:08,319] [INFO] Task started: Blastn
[2024-01-24 10:59:08,320] [INFO] Running command: blastn -query GCF_012062845.1_ASM1206284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1b9df13-2787-4d18-9e8b-3876ffa04931/dqc_reference/reference_markers_gtdb.fasta -out GCF_012062845.1_ASM1206284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,914] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,918] [INFO] Selected 6 target genomes.
[2024-01-24 10:59:09,918] [INFO] Target genome list was writen to GCF_012062845.1_ASM1206284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,925] [INFO] Task started: fastANI
[2024-01-24 10:59:09,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f004cf3-3fb2-4840-a026-8825b1191a25/GCF_012062845.1_ASM1206284v1_genomic.fna.gz --refList GCF_012062845.1_ASM1206284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012062845.1_ASM1206284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:15,390] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:15,404] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:15,404] [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_012062845.1	s__Halomonas_E sp012062845	100.0	1106	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004798965.1	s__Halomonas_E niordiana	93.4392	933	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268885.1	s__Halomonas_E taeanensis_A	84.9328	822	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014840935.1	s__Halomonas_E sp014840935	84.808	785	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013349955.1	s__Halomonas_E taeanensis_B	84.3052	789	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100755.1	s__Halomonas_E taeanensis	84.2089	787	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:15,406] [INFO] GTDB search result was written to GCF_012062845.1_ASM1206284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:15,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:15,412] [INFO] DFAST_QC result json was written to GCF_012062845.1_ASM1206284v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:15,412] [INFO] DFAST_QC completed!
[2024-01-24 10:59:15,413] [INFO] Total running time: 0h1m9s