[2024-01-25 17:51:35,486] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference
[2024-01-25 17:51:36,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,632] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b636dbc-8a8d-4f4a-bd52-6771bff697f8/GCF_020164585.1_ASM2016458v1_genomic.fna.gz | prodigal -d GCF_020164585.1_ASM2016458v1_genomic.fna/cds.fna -a GCF_020164585.1_ASM2016458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:46,057] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:46,057] [INFO] Task started: HMMsearch
[2024-01-25 17:51:46,057] [INFO] Running command: hmmsearch --tblout GCF_020164585.1_ASM2016458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/reference_markers.hmm GCF_020164585.1_ASM2016458v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:46,314] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:46,315] [INFO] Found 6/6 markers.
[2024-01-25 17:51:46,340] [INFO] Query marker FASTA was written to GCF_020164585.1_ASM2016458v1_genomic.fna/markers.fasta
[2024-01-25 17:51:46,340] [INFO] Task started: Blastn
[2024-01-25 17:51:46,340] [INFO] Running command: blastn -query GCF_020164585.1_ASM2016458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/reference_markers.fasta -out GCF_020164585.1_ASM2016458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:46,941] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:46,944] [INFO] Selected 14 target genomes.
[2024-01-25 17:51:46,944] [INFO] Target genome list was writen to GCF_020164585.1_ASM2016458v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:46,978] [INFO] Task started: fastANI
[2024-01-25 17:51:46,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b636dbc-8a8d-4f4a-bd52-6771bff697f8/GCF_020164585.1_ASM2016458v1_genomic.fna.gz --refList GCF_020164585.1_ASM2016458v1_genomic.fna/target_genomes.txt --output GCF_020164585.1_ASM2016458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:56,003] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:56,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:56,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:56,009] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:51:56,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:51:56,010] [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 sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	82.7443	693	991	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	82.4768	684	991	95	below_threshold
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	79.6703	467	991	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	78.5458	332	991	95	below_threshold
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	78.3927	328	991	95	below_threshold
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	77.9374	321	991	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.4699	59	991	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:56,012] [INFO] DFAST Taxonomy check result was written to GCF_020164585.1_ASM2016458v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:56,013] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:56,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:56,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/checkm_data
[2024-01-25 17:51:56,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:56,045] [INFO] Task started: CheckM
[2024-01-25 17:51:56,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020164585.1_ASM2016458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020164585.1_ASM2016458v1_genomic.fna/checkm_input GCF_020164585.1_ASM2016458v1_genomic.fna/checkm_result
[2024-01-25 17:52:27,318] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:27,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:27,334] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:27,334] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:27,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020164585.1_ASM2016458v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:27,335] [INFO] Task started: Blastn
[2024-01-25 17:52:27,335] [INFO] Running command: blastn -query GCF_020164585.1_ASM2016458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b659e1d-90c6-40ec-bbdc-71989ea560b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_020164585.1_ASM2016458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:28,177] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:28,186] [INFO] Selected 14 target genomes.
[2024-01-25 17:52:28,187] [INFO] Target genome list was writen to GCF_020164585.1_ASM2016458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:28,202] [INFO] Task started: fastANI
[2024-01-25 17:52:28,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b636dbc-8a8d-4f4a-bd52-6771bff697f8/GCF_020164585.1_ASM2016458v1_genomic.fna.gz --refList GCF_020164585.1_ASM2016458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020164585.1_ASM2016458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:36,469] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:36,476] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:52:36,476] [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_900099815.1	s__Psychroflexus sediminis	82.7276	694	991	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	82.4767	684	991	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	78.542	333	991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355905.1	s__Psychroflexus gondwanensis	78.3927	328	991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	-
GCA_003565575.1	s__Psychroflexus sp003565575	78.3648	227	991	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	77.9521	284	991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153485.2	s__Psychroflexus torquis	77.9345	322	991	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	77.5869	198	991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	76.0231	64	991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:36,478] [INFO] GTDB search result was written to GCF_020164585.1_ASM2016458v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:36,478] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:36,481] [INFO] DFAST_QC result json was written to GCF_020164585.1_ASM2016458v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:36,481] [INFO] DFAST_QC completed!
[2024-01-25 17:52:36,481] [INFO] Total running time: 0h1m1s