[2024-01-24 13:02:03,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference
[2024-01-24 13:02:05,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,016] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg73182b04-c122-46b8-b2f9-9ffd4da3705a/GCF_007751715.1_ASM775171v1_genomic.fna.gz | prodigal -d GCF_007751715.1_ASM775171v1_genomic.fna/cds.fna -a GCF_007751715.1_ASM775171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:48,100] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:48,100] [INFO] Task started: HMMsearch
[2024-01-24 13:02:48,100] [INFO] Running command: hmmsearch --tblout GCF_007751715.1_ASM775171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/reference_markers.hmm GCF_007751715.1_ASM775171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:48,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:48,544] [INFO] Found 6/6 markers.
[2024-01-24 13:02:48,604] [INFO] Query marker FASTA was written to GCF_007751715.1_ASM775171v1_genomic.fna/markers.fasta
[2024-01-24 13:02:48,604] [INFO] Task started: Blastn
[2024-01-24 13:02:48,604] [INFO] Running command: blastn -query GCF_007751715.1_ASM775171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/reference_markers.fasta -out GCF_007751715.1_ASM775171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:49,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:49,217] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:49,218] [INFO] Target genome list was writen to GCF_007751715.1_ASM775171v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:49,230] [INFO] Task started: fastANI
[2024-01-24 13:02:49,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg73182b04-c122-46b8-b2f9-9ffd4da3705a/GCF_007751715.1_ASM775171v1_genomic.fna.gz --refList GCF_007751715.1_ASM775171v1_genomic.fna/target_genomes.txt --output GCF_007751715.1_ASM775171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:12,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:12,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:12,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:12,036] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:12,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:12,037] [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 oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	100.0	2416	2416	95	conclusive
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	91.2516	1962	2416	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	88.5056	1830	2416	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.6414	140	2416	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	76.4374	124	2416	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.3879	145	2416	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	76.3664	190	2416	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	76.3469	192	2416	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	76.2773	129	2416	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.2684	148	2416	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.0293	206	2416	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	75.9443	152	2416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:12,040] [INFO] DFAST Taxonomy check result was written to GCF_007751715.1_ASM775171v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:12,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:12,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:12,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/checkm_data
[2024-01-24 13:03:12,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:12,111] [INFO] Task started: CheckM
[2024-01-24 13:03:12,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007751715.1_ASM775171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007751715.1_ASM775171v1_genomic.fna/checkm_input GCF_007751715.1_ASM775171v1_genomic.fna/checkm_result
[2024-01-24 13:04:57,690] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:57,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:57,716] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:57,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:57,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007751715.1_ASM775171v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:57,717] [INFO] Task started: Blastn
[2024-01-24 13:04:57,717] [INFO] Running command: blastn -query GCF_007751715.1_ASM775171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2a49a42-3b7d-431c-a888-e70733aed4a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007751715.1_ASM775171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:58,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:58,537] [INFO] Selected 15 target genomes.
[2024-01-24 13:04:58,537] [INFO] Target genome list was writen to GCF_007751715.1_ASM775171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:58,585] [INFO] Task started: fastANI
[2024-01-24 13:04:58,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg73182b04-c122-46b8-b2f9-9ffd4da3705a/GCF_007751715.1_ASM775171v1_genomic.fna.gz --refList GCF_007751715.1_ASM775171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007751715.1_ASM775171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:05:20,504] [INFO] Task succeeded: fastANI
[2024-01-24 13:05:20,518] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:05:20,518] [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_007751715.1	s__Rosistilla oblonga	100.0	2416	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	conclusive
GCA_007741475.1	s__Rosistilla sp007741475	91.2514	1962	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753095.1	s__Rosistilla carotiformis	88.5136	1827	2416	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	76.3879	145	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_008065135.1	s__Roseimaritima ulvae	76.3469	192	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010367455.1	s__Laterigemmans baculatus	76.2912	165	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007860105.1	s__Rhodopirellula sp007860105	76.1999	82	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	76.111	202	2416	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	76.0293	206	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	75.9367	153	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	75.8965	185	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	75.8663	136	2416	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	75.8516	213	2416	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:05:20,520] [INFO] GTDB search result was written to GCF_007751715.1_ASM775171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:05:20,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:05:20,524] [INFO] DFAST_QC result json was written to GCF_007751715.1_ASM775171v1_genomic.fna/dqc_result.json
[2024-01-24 13:05:20,524] [INFO] DFAST_QC completed!
[2024-01-24 13:05:20,524] [INFO] Total running time: 0h3m17s