[2024-01-24 13:57:13,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference
[2024-01-24 13:57:15,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,015] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg44816e95-9251-4bb5-bab6-ccdaa29a9ed6/GCF_000355905.1_Pgondw1.0_genomic.fna.gz | prodigal -d GCF_000355905.1_Pgondw1.0_genomic.fna/cds.fna -a GCF_000355905.1_Pgondw1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:26,503] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:26,503] [INFO] Task started: HMMsearch
[2024-01-24 13:57:26,503] [INFO] Running command: hmmsearch --tblout GCF_000355905.1_Pgondw1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/reference_markers.hmm GCF_000355905.1_Pgondw1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:26,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:26,764] [INFO] Found 6/6 markers.
[2024-01-24 13:57:26,798] [INFO] Query marker FASTA was written to GCF_000355905.1_Pgondw1.0_genomic.fna/markers.fasta
[2024-01-24 13:57:26,799] [INFO] Task started: Blastn
[2024-01-24 13:57:26,799] [INFO] Running command: blastn -query GCF_000355905.1_Pgondw1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/reference_markers.fasta -out GCF_000355905.1_Pgondw1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:27,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:27,421] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:27,422] [INFO] Target genome list was writen to GCF_000355905.1_Pgondw1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:27,432] [INFO] Task started: fastANI
[2024-01-24 13:57:27,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg44816e95-9251-4bb5-bab6-ccdaa29a9ed6/GCF_000355905.1_Pgondw1.0_genomic.fna.gz --refList GCF_000355905.1_Pgondw1.0_genomic.fna/target_genomes.txt --output GCF_000355905.1_Pgondw1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:35,904] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:35,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:35,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:35,915] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:35,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:35,916] [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
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	100.0	1072	1075	95	conclusive
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	90.5529	899	1075	95	below_threshold
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	81.4536	424	1075	95	below_threshold
Psychroflexus sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	78.0091	315	1075	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	77.9686	283	1075	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	77.8305	297	1075	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.4275	73	1075	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	76.3593	68	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:35,918] [INFO] DFAST Taxonomy check result was written to GCF_000355905.1_Pgondw1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:57:35,919] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:35,919] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:35,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/checkm_data
[2024-01-24 13:57:35,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:35,954] [INFO] Task started: CheckM
[2024-01-24 13:57:35,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000355905.1_Pgondw1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000355905.1_Pgondw1.0_genomic.fna/checkm_input GCF_000355905.1_Pgondw1.0_genomic.fna/checkm_result
[2024-01-24 13:58:14,547] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:14,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:14,581] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:14,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:14,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000355905.1_Pgondw1.0_genomic.fna/markers.fasta)
[2024-01-24 13:58:14,582] [INFO] Task started: Blastn
[2024-01-24 13:58:14,582] [INFO] Running command: blastn -query GCF_000355905.1_Pgondw1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f11ed7-b981-416b-94f6-d9aa1c0c731b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000355905.1_Pgondw1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:15,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:15,458] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:15,458] [INFO] Target genome list was writen to GCF_000355905.1_Pgondw1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:15,466] [INFO] Task started: fastANI
[2024-01-24 13:58:15,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg44816e95-9251-4bb5-bab6-ccdaa29a9ed6/GCF_000355905.1_Pgondw1.0_genomic.fna.gz --refList GCF_000355905.1_Pgondw1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000355905.1_Pgondw1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:23,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:23,245] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:23,246] [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_000355905.1	s__Psychroflexus gondwanensis	100.0	1072	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	conclusive
GCF_000153485.2	s__Psychroflexus torquis	90.5377	900	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836055.1	s__Psychroflexus sp002836055	90.0349	792	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099815.1	s__Psychroflexus sediminis	78.0053	314	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820555.1	s__Psychroflexus sp010820555	77.9724	284	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378765.1	s__Psychroflexus tropicus	77.8414	296	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565575.1	s__Psychroflexus sp003565575	77.6527	187	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010055.1	s__Psychroflexus aestuariivivens	77.3999	216	1075	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,247] [INFO] GTDB search result was written to GCF_000355905.1_Pgondw1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:23,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:23,252] [INFO] DFAST_QC result json was written to GCF_000355905.1_Pgondw1.0_genomic.fna/dqc_result.json
[2024-01-24 13:58:23,252] [INFO] DFAST_QC completed!
[2024-01-24 13:58:23,252] [INFO] Total running time: 0h1m10s