[2024-01-24 12:36:23,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:23,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:23,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference
[2024-01-24 12:36:25,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,180] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg6883f47c-cacb-41cd-971b-4aa65ced6f7a/GCF_012070355.1_ASM1207035v1_genomic.fna.gz | prodigal -d GCF_012070355.1_ASM1207035v1_genomic.fna/cds.fna -a GCF_012070355.1_ASM1207035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:36,874] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:36,874] [INFO] Task started: HMMsearch
[2024-01-24 12:36:36,875] [INFO] Running command: hmmsearch --tblout GCF_012070355.1_ASM1207035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/reference_markers.hmm GCF_012070355.1_ASM1207035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:37,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:37,142] [INFO] Found 6/6 markers.
[2024-01-24 12:36:37,177] [INFO] Query marker FASTA was written to GCF_012070355.1_ASM1207035v1_genomic.fna/markers.fasta
[2024-01-24 12:36:37,178] [INFO] Task started: Blastn
[2024-01-24 12:36:37,178] [INFO] Running command: blastn -query GCF_012070355.1_ASM1207035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/reference_markers.fasta -out GCF_012070355.1_ASM1207035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:37,999] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:38,003] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:38,003] [INFO] Target genome list was writen to GCF_012070355.1_ASM1207035v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:38,010] [INFO] Task started: fastANI
[2024-01-24 12:36:38,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg6883f47c-cacb-41cd-971b-4aa65ced6f7a/GCF_012070355.1_ASM1207035v1_genomic.fna.gz --refList GCF_012070355.1_ASM1207035v1_genomic.fna/target_genomes.txt --output GCF_012070355.1_ASM1207035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:48,729] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:48,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:48,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:48,748] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:36:48,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:48,748] [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
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	100.0	1308	1308	95	conclusive
Marinobacter daqiaonensis	strain=CGMCC 1.9167	GCA_900115285.1	650891	650891	type	True	99.9936	1305	1308	95	conclusive
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	80.5037	629	1308	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	80.4446	722	1308	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	80.3837	662	1308	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.1973	436	1308	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	78.861	338	1308	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.8072	378	1308	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	78.7927	362	1308	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.762	375	1308	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.6836	391	1308	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.6357	354	1308	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.5321	401	1308	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.3347	76	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:48,750] [INFO] DFAST Taxonomy check result was written to GCF_012070355.1_ASM1207035v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:48,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:48,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:48,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/checkm_data
[2024-01-24 12:36:48,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:48,794] [INFO] Task started: CheckM
[2024-01-24 12:36:48,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012070355.1_ASM1207035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012070355.1_ASM1207035v1_genomic.fna/checkm_input GCF_012070355.1_ASM1207035v1_genomic.fna/checkm_result
[2024-01-24 12:37:25,915] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:25,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:25,937] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:25,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:25,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012070355.1_ASM1207035v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:25,938] [INFO] Task started: Blastn
[2024-01-24 12:37:25,939] [INFO] Running command: blastn -query GCF_012070355.1_ASM1207035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3efd7fe1-96b7-4012-9afe-e9dbfb818674/dqc_reference/reference_markers_gtdb.fasta -out GCF_012070355.1_ASM1207035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:27,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:27,301] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:27,301] [INFO] Target genome list was writen to GCF_012070355.1_ASM1207035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:27,314] [INFO] Task started: fastANI
[2024-01-24 12:37:27,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg6883f47c-cacb-41cd-971b-4aa65ced6f7a/GCF_012070355.1_ASM1207035v1_genomic.fna.gz --refList GCF_012070355.1_ASM1207035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012070355.1_ASM1207035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:39,392] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:39,409] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:39,409] [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_900115285.1	s__Marinobacter daqiaonensis	99.9936	1305	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900111555.1	s__Marinobacter segnicrescens	80.5126	628	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	80.418	726	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.2787	439	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	79.2009	437	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.0168	435	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	78.8306	361	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.8205	383	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201735.1	s__Marinobacter oulmenensis	78.8049	361	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	78.8019	379	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_003007715.1	s__Marinobacter shengliensis	78.6928	360	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_017301335.1	s__Marinobacter sp017301335	78.6565	284	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	78.5995	360	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	78.5337	348	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	78.375	301	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:39,411] [INFO] GTDB search result was written to GCF_012070355.1_ASM1207035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:39,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:39,416] [INFO] DFAST_QC result json was written to GCF_012070355.1_ASM1207035v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:39,416] [INFO] DFAST_QC completed!
[2024-01-24 12:37:39,416] [INFO] Total running time: 0h1m16s