[2024-01-24 11:12:55,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:55,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:55,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference
[2024-01-24 11:12:56,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:56,699] [INFO] Task started: Prodigal
[2024-01-24 11:12:56,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg35f3c61b-8528-41ad-8ae4-78d5f2031f5a/GCF_000690055.1_Afuliginea_genomic.fna.gz | prodigal -d GCF_000690055.1_Afuliginea_genomic.fna/cds.fna -a GCF_000690055.1_Afuliginea_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,396] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,396] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,396] [INFO] Running command: hmmsearch --tblout GCF_000690055.1_Afuliginea_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/reference_markers.hmm GCF_000690055.1_Afuliginea_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:05,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:05,777] [INFO] Found 6/6 markers.
[2024-01-24 11:13:05,822] [INFO] Query marker FASTA was written to GCF_000690055.1_Afuliginea_genomic.fna/markers.fasta
[2024-01-24 11:13:05,823] [INFO] Task started: Blastn
[2024-01-24 11:13:05,823] [INFO] Running command: blastn -query GCF_000690055.1_Afuliginea_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/reference_markers.fasta -out GCF_000690055.1_Afuliginea_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,558] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,560] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:06,561] [INFO] Target genome list was writen to GCF_000690055.1_Afuliginea_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,565] [INFO] Task started: fastANI
[2024-01-24 11:13:06,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg35f3c61b-8528-41ad-8ae4-78d5f2031f5a/GCF_000690055.1_Afuliginea_genomic.fna.gz --refList GCF_000690055.1_Afuliginea_genomic.fna/target_genomes.txt --output GCF_000690055.1_Afuliginea_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:17,847] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:17,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:17,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:17,857] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:17,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:17,857] [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
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	100.0	1496	1501	95	conclusive
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	91.2726	1139	1501	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	90.5676	1131	1501	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	87.7421	1097	1501	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	83.937	993	1501	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	82.5241	797	1501	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.0772	659	1501	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.9486	206	1501	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	77.1113	52	1501	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.7321	66	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:17,859] [INFO] DFAST Taxonomy check result was written to GCF_000690055.1_Afuliginea_genomic.fna/tc_result.tsv
[2024-01-24 11:13:17,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:17,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:17,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/checkm_data
[2024-01-24 11:13:17,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:17,906] [INFO] Task started: CheckM
[2024-01-24 11:13:17,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000690055.1_Afuliginea_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000690055.1_Afuliginea_genomic.fna/checkm_input GCF_000690055.1_Afuliginea_genomic.fna/checkm_result
[2024-01-24 11:13:49,736] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:49,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,758] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:49,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:49,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000690055.1_Afuliginea_genomic.fna/markers.fasta)
[2024-01-24 11:13:49,759] [INFO] Task started: Blastn
[2024-01-24 11:13:49,760] [INFO] Running command: blastn -query GCF_000690055.1_Afuliginea_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b70e83b-a847-4eae-b6f6-fbf315865ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000690055.1_Afuliginea_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,887] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,890] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:50,890] [INFO] Target genome list was writen to GCF_000690055.1_Afuliginea_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,898] [INFO] Task started: fastANI
[2024-01-24 11:13:50,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg35f3c61b-8528-41ad-8ae4-78d5f2031f5a/GCF_000690055.1_Afuliginea_genomic.fna.gz --refList GCF_000690055.1_Afuliginea_genomic.fna/target_genomes_gtdb.txt --output GCF_000690055.1_Afuliginea_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:01,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:01,531] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:01,532] [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_000690055.1	s__Pseudoalteromonas fuliginea	100.0	1496	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	conclusive
GCA_000814675.1	s__Pseudoalteromonas distincta	91.2875	1138	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_000238395.3	s__Pseudoalteromonas arctica	90.571	1131	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	90.2777	1120	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	89.7889	1144	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	89.4248	1117	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	89.297	998	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905615.1	s__Pseudoalteromonas aliena	87.7474	1097	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:01,533] [INFO] GTDB search result was written to GCF_000690055.1_Afuliginea_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:01,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:01,536] [INFO] DFAST_QC result json was written to GCF_000690055.1_Afuliginea_genomic.fna/dqc_result.json
[2024-01-24 11:14:01,536] [INFO] DFAST_QC completed!
[2024-01-24 11:14:01,537] [INFO] Total running time: 0h1m6s