[2024-01-24 14:40:02,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference
[2024-01-24 14:40:03,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,652] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,653] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d3410af-dc44-42de-a458-61188bd73474/GCF_007741475.1_ASM774147v1_genomic.fna.gz | prodigal -d GCF_007741475.1_ASM774147v1_genomic.fna/cds.fna -a GCF_007741475.1_ASM774147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:41:00,613] [INFO] Task succeeded: Prodigal
[2024-01-24 14:41:00,614] [INFO] Task started: HMMsearch
[2024-01-24 14:41:00,614] [INFO] Running command: hmmsearch --tblout GCF_007741475.1_ASM774147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/reference_markers.hmm GCF_007741475.1_ASM774147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:41:00,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:41:00,977] [INFO] Found 6/6 markers.
[2024-01-24 14:41:01,034] [INFO] Query marker FASTA was written to GCF_007741475.1_ASM774147v1_genomic.fna/markers.fasta
[2024-01-24 14:41:01,035] [INFO] Task started: Blastn
[2024-01-24 14:41:01,035] [INFO] Running command: blastn -query GCF_007741475.1_ASM774147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/reference_markers.fasta -out GCF_007741475.1_ASM774147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:01,654] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:01,660] [INFO] Selected 13 target genomes.
[2024-01-24 14:41:01,661] [INFO] Target genome list was writen to GCF_007741475.1_ASM774147v1_genomic.fna/target_genomes.txt
[2024-01-24 14:41:01,670] [INFO] Task started: fastANI
[2024-01-24 14:41:01,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d3410af-dc44-42de-a458-61188bd73474/GCF_007741475.1_ASM774147v1_genomic.fna.gz --refList GCF_007741475.1_ASM774147v1_genomic.fna/target_genomes.txt --output GCF_007741475.1_ASM774147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:41:20,892] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:20,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:41:20,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:41:20,913] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:41:20,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:41:20,913] [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
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	100.0	2489	2491	95	conclusive
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	91.301	1959	2491	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	88.7039	1934	2491	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.5337	137	2491	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	76.4649	133	2491	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.4359	144	2491	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.2297	121	2491	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	76.1564	110	2491	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.9137	184	2491	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.8984	198	2491	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.7381	135	2491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:41:20,915] [INFO] DFAST Taxonomy check result was written to GCF_007741475.1_ASM774147v1_genomic.fna/tc_result.tsv
[2024-01-24 14:41:20,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:41:20,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:41:20,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/checkm_data
[2024-01-24 14:41:20,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:41:20,994] [INFO] Task started: CheckM
[2024-01-24 14:41:20,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007741475.1_ASM774147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007741475.1_ASM774147v1_genomic.fna/checkm_input GCF_007741475.1_ASM774147v1_genomic.fna/checkm_result
[2024-01-24 14:43:39,281] [INFO] Task succeeded: CheckM
[2024-01-24 14:43:39,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:43:39,307] [INFO] ===== Completeness check finished =====
[2024-01-24 14:43:39,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:43:39,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007741475.1_ASM774147v1_genomic.fna/markers.fasta)
[2024-01-24 14:43:39,308] [INFO] Task started: Blastn
[2024-01-24 14:43:39,308] [INFO] Running command: blastn -query GCF_007741475.1_ASM774147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f234cf4-ff05-4e39-b874-8e0f40cb6948/dqc_reference/reference_markers_gtdb.fasta -out GCF_007741475.1_ASM774147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:43:40,128] [INFO] Task succeeded: Blastn
[2024-01-24 14:43:40,133] [INFO] Selected 14 target genomes.
[2024-01-24 14:43:40,133] [INFO] Target genome list was writen to GCF_007741475.1_ASM774147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:43:40,155] [INFO] Task started: fastANI
[2024-01-24 14:43:40,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d3410af-dc44-42de-a458-61188bd73474/GCF_007741475.1_ASM774147v1_genomic.fna.gz --refList GCF_007741475.1_ASM774147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007741475.1_ASM774147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:59,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:59,437] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:59,437] [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
GCA_007741475.1	s__Rosistilla sp007741475	100.0	2489	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007751715.1	s__Rosistilla oblonga	91.2826	1960	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	-
GCF_007753095.1	s__Rosistilla carotiformis	88.691	1936	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	76.5337	137	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_010367455.1	s__Laterigemmans baculatus	76.2848	158	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000196115.1	s__Rhodopirellula baltica	76.2451	120	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_007859855.1	s__Rhodopirellula solitaria	76.1564	110	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	76.1416	149	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.0775	191	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	75.9066	185	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	75.6251	192	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127095.1	s__UBA6163 sp007127095	75.4469	116	2491	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	99.08	99.08	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:59,439] [INFO] GTDB search result was written to GCF_007741475.1_ASM774147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:59,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:59,444] [INFO] DFAST_QC result json was written to GCF_007741475.1_ASM774147v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:59,444] [INFO] DFAST_QC completed!
[2024-01-24 14:43:59,444] [INFO] Total running time: 0h3m57s