[2024-01-24 13:35:27,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference
[2024-01-24 13:35:28,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,557] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg82166aa9-cca0-4997-845b-bb5cfd2cdf1a/GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/cds.fna -a GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:02,217] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:02,218] [INFO] Task started: HMMsearch
[2024-01-24 13:36:02,218] [INFO] Running command: hmmsearch --tblout GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/reference_markers.hmm GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:02,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:02,589] [INFO] Found 6/6 markers.
[2024-01-24 13:36:02,654] [INFO] Query marker FASTA was written to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:36:02,655] [INFO] Task started: Blastn
[2024-01-24 13:36:02,655] [INFO] Running command: blastn -query GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/reference_markers.fasta -out GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:03,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:03,277] [INFO] Selected 16 target genomes.
[2024-01-24 13:36:03,278] [INFO] Target genome list was writen to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:36:03,298] [INFO] Task started: fastANI
[2024-01-24 13:36:03,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg82166aa9-cca0-4997-845b-bb5cfd2cdf1a/GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna.gz --refList GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:19,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:19,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:19,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:19,405] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:19,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:19,405] [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
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	100.0	2660	2663	95	conclusive
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	84.7023	1690	2663	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	81.1833	769	2663	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	79.3327	492	2663	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	79.1771	485	2663	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.9846	385	2663	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.8078	392	2663	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	78.7625	418	2663	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	78.7306	382	2663	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.2337	350	2663	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	78.1323	188	2663	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.592	136	2663	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.6202	59	2663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:19,407] [INFO] DFAST Taxonomy check result was written to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:36:19,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:19,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:19,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/checkm_data
[2024-01-24 13:36:19,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:19,479] [INFO] Task started: CheckM
[2024-01-24 13:36:19,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/checkm_input GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:37:53,263] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:53,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,290] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:53,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:53,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:37:53,291] [INFO] Task started: Blastn
[2024-01-24 13:37:53,291] [INFO] Running command: blastn -query GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b3a8c0-cfac-4804-bdb8-b3c19dd30efb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:54,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:54,201] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:54,202] [INFO] Target genome list was writen to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:54,211] [INFO] Task started: fastANI
[2024-01-24 13:37:54,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg82166aa9-cca0-4997-845b-bb5cfd2cdf1a/GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna.gz --refList GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:06,365] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:06,373] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:06,373] [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_900103665.1	s__Pedobacter steynii	100.0	2660	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003852525.1	s__Pedobacter sp003852525	88.8817	1998	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	84.6972	1691	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721645.1	s__Pedobacter steynii_A	83.9161	1489	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014472395.1	s__Pedobacter sp014472395	81.2788	785	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412655.1	s__Pedobacter sp001412655	81.2139	816	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172405.1	s__Pedobacter gandavensis	81.1657	771	2663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,376] [INFO] GTDB search result was written to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:06,377] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:06,381] [INFO] DFAST_QC result json was written to GCF_900103665.1_IMG-taxon_2675903693_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:38:06,381] [INFO] DFAST_QC completed!
[2024-01-24 13:38:06,382] [INFO] Total running time: 0h2m39s