[2024-01-24 13:17:13,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference
[2024-01-24 13:17:15,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,037] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg39b8c286-6b97-4f85-91c7-20221ea63a41/GCF_007753095.1_ASM775309v1_genomic.fna.gz | prodigal -d GCF_007753095.1_ASM775309v1_genomic.fna/cds.fna -a GCF_007753095.1_ASM775309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:02,788] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:02,789] [INFO] Task started: HMMsearch
[2024-01-24 13:18:02,789] [INFO] Running command: hmmsearch --tblout GCF_007753095.1_ASM775309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/reference_markers.hmm GCF_007753095.1_ASM775309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:03,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:03,169] [INFO] Found 6/6 markers.
[2024-01-24 13:18:03,225] [INFO] Query marker FASTA was written to GCF_007753095.1_ASM775309v1_genomic.fna/markers.fasta
[2024-01-24 13:18:03,226] [INFO] Task started: Blastn
[2024-01-24 13:18:03,226] [INFO] Running command: blastn -query GCF_007753095.1_ASM775309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/reference_markers.fasta -out GCF_007753095.1_ASM775309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,868] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,873] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:03,874] [INFO] Target genome list was writen to GCF_007753095.1_ASM775309v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:03,885] [INFO] Task started: fastANI
[2024-01-24 13:18:03,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b8c286-6b97-4f85-91c7-20221ea63a41/GCF_007753095.1_ASM775309v1_genomic.fna.gz --refList GCF_007753095.1_ASM775309v1_genomic.fna/target_genomes.txt --output GCF_007753095.1_ASM775309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:23,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:23,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:23,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:23,979] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:23,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:23,980] [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 carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	100.0	2479	2479	95	conclusive
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	88.7836	1913	2479	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	88.4423	1852	2479	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.3521	136	2479	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.3503	132	2479	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.0311	149	2479	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	77.0128	177	2479	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	76.9888	182	2479	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.8803	149	2479	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.3707	137	2479	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.1624	168	2479	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.1476	164	2479	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.0691	180	2479	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,981] [INFO] DFAST Taxonomy check result was written to GCF_007753095.1_ASM775309v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:23,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:23,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:23,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/checkm_data
[2024-01-24 13:18:23,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:24,051] [INFO] Task started: CheckM
[2024-01-24 13:18:24,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007753095.1_ASM775309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007753095.1_ASM775309v1_genomic.fna/checkm_input GCF_007753095.1_ASM775309v1_genomic.fna/checkm_result
[2024-01-24 13:20:29,365] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:29,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:29,397] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:29,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:29,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007753095.1_ASM775309v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:29,399] [INFO] Task started: Blastn
[2024-01-24 13:20:29,399] [INFO] Running command: blastn -query GCF_007753095.1_ASM775309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0010e806-a0f7-4e4c-8064-82a25faf9f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007753095.1_ASM775309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:30,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:30,198] [INFO] Selected 16 target genomes.
[2024-01-24 13:20:30,198] [INFO] Target genome list was writen to GCF_007753095.1_ASM775309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:30,210] [INFO] Task started: fastANI
[2024-01-24 13:20:30,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b8c286-6b97-4f85-91c7-20221ea63a41/GCF_007753095.1_ASM775309v1_genomic.fna.gz --refList GCF_007753095.1_ASM775309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007753095.1_ASM775309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:53,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:53,028] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:53,028] [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_007753095.1	s__Rosistilla carotiformis	100.0	2479	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007741475.1	s__Rosistilla sp007741475	88.7911	1912	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007751715.1	s__Rosistilla oblonga	88.4413	1851	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	-
GCF_014192335.1	s__Rhodopirellula rubra	77.3503	132	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_007752935.1	s__Crateriforma conspicua	77.0311	149	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_012290005.1	s__Crateriforma spongiae	76.8955	148	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_007753675.1	s__Stieleria sp007753675	76.5942	208	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	76.5162	147	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009618275.1	s__Roseimaritima sp009618275	76.1368	165	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.1307	181	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901265.1	s__Stieleria baltica_A	76.0362	117	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002289565.1	s__Stieleria sp002289565	75.9474	190	2479	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	75.9079	125	2479	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	75.7778	107	2479	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 13:20:53,030] [INFO] GTDB search result was written to GCF_007753095.1_ASM775309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:53,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:53,036] [INFO] DFAST_QC result json was written to GCF_007753095.1_ASM775309v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:53,036] [INFO] DFAST_QC completed!
[2024-01-24 13:20:53,036] [INFO] Total running time: 0h3m39s