[2024-01-24 13:31:35,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference
[2024-01-24 13:31:36,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,935] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg10cc6e7d-b6b2-4fec-b9ec-0b78d88cd5bd/GCF_004798965.1_ASM479896v1_genomic.fna.gz | prodigal -d GCF_004798965.1_ASM479896v1_genomic.fna/cds.fna -a GCF_004798965.1_ASM479896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,252] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,252] [INFO] Running command: hmmsearch --tblout GCF_004798965.1_ASM479896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/reference_markers.hmm GCF_004798965.1_ASM479896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,566] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,614] [INFO] Query marker FASTA was written to GCF_004798965.1_ASM479896v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,614] [INFO] Task started: Blastn
[2024-01-24 13:31:48,614] [INFO] Running command: blastn -query GCF_004798965.1_ASM479896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/reference_markers.fasta -out GCF_004798965.1_ASM479896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,631] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:49,632] [INFO] Target genome list was writen to GCF_004798965.1_ASM479896v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,636] [INFO] Task started: fastANI
[2024-01-24 13:31:49,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cc6e7d-b6b2-4fec-b9ec-0b78d88cd5bd/GCF_004798965.1_ASM479896v1_genomic.fna.gz --refList GCF_004798965.1_ASM479896v1_genomic.fna/target_genomes.txt --output GCF_004798965.1_ASM479896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:03,906] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:03,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:03,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:03,921] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:03,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:03,921] [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	100.0	1203	1204	95	conclusive
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	84.4277	915	1204	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	80.6572	577	1204	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	80.5102	611	1204	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	80.3812	567	1204	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	80.2459	554	1204	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	80.0547	550	1204	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.0474	586	1204	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	79.7333	479	1204	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.7189	550	1204	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	79.6997	524	1204	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	79.674	535	1204	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.622	541	1204	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.6198	473	1204	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.5334	490	1204	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	79.4579	495	1204	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.3997	499	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:03,923] [INFO] DFAST Taxonomy check result was written to GCF_004798965.1_ASM479896v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:03,923] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:03,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:03,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/checkm_data
[2024-01-24 13:32:03,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:03,962] [INFO] Task started: CheckM
[2024-01-24 13:32:03,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004798965.1_ASM479896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004798965.1_ASM479896v1_genomic.fna/checkm_input GCF_004798965.1_ASM479896v1_genomic.fna/checkm_result
[2024-01-24 13:32:40,975] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:40,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:40,994] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:40,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:40,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004798965.1_ASM479896v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:40,995] [INFO] Task started: Blastn
[2024-01-24 13:32:40,996] [INFO] Running command: blastn -query GCF_004798965.1_ASM479896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccca3904-3baf-4afb-b15f-a79a785c6a6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004798965.1_ASM479896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:42,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:42,711] [INFO] Selected 6 target genomes.
[2024-01-24 13:32:42,711] [INFO] Target genome list was writen to GCF_004798965.1_ASM479896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:42,718] [INFO] Task started: fastANI
[2024-01-24 13:32:42,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cc6e7d-b6b2-4fec-b9ec-0b78d88cd5bd/GCF_004798965.1_ASM479896v1_genomic.fna.gz --refList GCF_004798965.1_ASM479896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004798965.1_ASM479896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:49,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,040] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:49,040] [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_004798965.1	s__Halomonas_E niordiana	100.0	1203	1204	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_012062845.1	s__Halomonas_E sp012062845	93.32	940	1204	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	85.1131	939	1204	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	84.7259	927	1204	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	84.6084	848	1204	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	84.4296	914	1204	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 13:32:49,042] [INFO] GTDB search result was written to GCF_004798965.1_ASM479896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:49,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:49,046] [INFO] DFAST_QC result json was written to GCF_004798965.1_ASM479896v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:49,046] [INFO] DFAST_QC completed!
[2024-01-24 13:32:49,046] [INFO] Total running time: 0h1m14s