[2024-01-24 15:19:49,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:49,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:49,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference
[2024-01-24 15:19:50,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:50,275] [INFO] Task started: Prodigal
[2024-01-24 15:19:50,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg29b7d4bb-47d0-40fe-8b2d-8a073ec9db89/GCF_002646595.1_ASM264659v1_genomic.fna.gz | prodigal -d GCF_002646595.1_ASM264659v1_genomic.fna/cds.fna -a GCF_002646595.1_ASM264659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:45,778] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:45,779] [INFO] Task started: HMMsearch
[2024-01-24 15:20:45,779] [INFO] Running command: hmmsearch --tblout GCF_002646595.1_ASM264659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/reference_markers.hmm GCF_002646595.1_ASM264659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:46,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:46,261] [INFO] Found 6/6 markers.
[2024-01-24 15:20:46,343] [INFO] Query marker FASTA was written to GCF_002646595.1_ASM264659v1_genomic.fna/markers.fasta
[2024-01-24 15:20:46,343] [INFO] Task started: Blastn
[2024-01-24 15:20:46,344] [INFO] Running command: blastn -query GCF_002646595.1_ASM264659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/reference_markers.fasta -out GCF_002646595.1_ASM264659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:46,979] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:46,981] [INFO] Selected 20 target genomes.
[2024-01-24 15:20:46,982] [INFO] Target genome list was writen to GCF_002646595.1_ASM264659v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:47,002] [INFO] Task started: fastANI
[2024-01-24 15:20:47,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg29b7d4bb-47d0-40fe-8b2d-8a073ec9db89/GCF_002646595.1_ASM264659v1_genomic.fna.gz --refList GCF_002646595.1_ASM264659v1_genomic.fna/target_genomes.txt --output GCF_002646595.1_ASM264659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:21:06,553] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:06,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:21:06,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:21:06,572] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:21:06,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:21:06,572] [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
Flavilitoribacter nigricans	strain=NBRC 102662	GCA_002646595.1	70997	70997	type	True	100.0	3710	3714	95	conclusive
Phaeodactylibacter xiamenensis	strain=KD52	GCA_000759025.1	1524460	1524460	type	True	75.87	85	3714	95	below_threshold
Phaeodactylibacter luteus	strain=KCTC 42180	GCA_007993045.1	1564516	1564516	type	True	75.7677	56	3714	95	below_threshold
Lewinella cohaerens	strain=DSM 23179	GCA_000379805.1	70995	70995	type	True	75.3972	57	3714	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.3701	71	3714	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	75.3635	58	3714	95	below_threshold
Haliscomenobacter hydrossis	strain=DSM 1100	GCA_000212735.1	2350	2350	type	True	75.3607	72	3714	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.3564	72	3714	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	74.8203	50	3714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:21:06,574] [INFO] DFAST Taxonomy check result was written to GCF_002646595.1_ASM264659v1_genomic.fna/tc_result.tsv
[2024-01-24 15:21:06,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:21:06,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:21:06,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/checkm_data
[2024-01-24 15:21:06,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:21:06,678] [INFO] Task started: CheckM
[2024-01-24 15:21:06,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002646595.1_ASM264659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002646595.1_ASM264659v1_genomic.fna/checkm_input GCF_002646595.1_ASM264659v1_genomic.fna/checkm_result
[2024-01-24 15:23:29,180] [INFO] Task succeeded: CheckM
[2024-01-24 15:23:29,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:23:29,209] [INFO] ===== Completeness check finished =====
[2024-01-24 15:23:29,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:23:29,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002646595.1_ASM264659v1_genomic.fna/markers.fasta)
[2024-01-24 15:23:29,211] [INFO] Task started: Blastn
[2024-01-24 15:23:29,211] [INFO] Running command: blastn -query GCF_002646595.1_ASM264659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f85a528-c199-43ba-b5e4-246eb4828732/dqc_reference/reference_markers_gtdb.fasta -out GCF_002646595.1_ASM264659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:23:30,603] [INFO] Task succeeded: Blastn
[2024-01-24 15:23:30,607] [INFO] Selected 25 target genomes.
[2024-01-24 15:23:30,608] [INFO] Target genome list was writen to GCF_002646595.1_ASM264659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:23:30,628] [INFO] Task started: fastANI
[2024-01-24 15:23:30,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg29b7d4bb-47d0-40fe-8b2d-8a073ec9db89/GCF_002646595.1_ASM264659v1_genomic.fna.gz --refList GCF_002646595.1_ASM264659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002646595.1_ASM264659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:23:58,881] [INFO] Task succeeded: fastANI
[2024-01-24 15:23:58,987] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:23:58,987] [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_002646595.1	s__Flavilitoribacter nigricans	100.0	3710	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Flavilitoribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000759025.1	s__Phaeodactylibacter xiamenensis	75.87	85	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993045.1	s__Phaeodactylibacter luteus	75.7677	56	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222965.1	s__JAAEZH01 sp018222965	75.6146	61	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JAAEZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045895.1	s__Lewinella sp003045895	75.559	71	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella	95.0	99.87	99.87	0.95	0.95	2	-
GCA_016711045.1	s__JADJTT01 sp016711045	75.4686	60	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	99.22	99.22	0.93	0.93	2	-
GCA_016703765.1	s__JADJTT01 sp016703765	75.4433	63	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JADJTT01	95.0	98.25	98.24	0.94	0.92	3	-
GCF_000379805.1	s__Lewinella cohaerens	75.3972	57	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212735.1	s__Haliscomenobacter hydrossis	75.3828	73	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Haliscomenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	75.3701	71	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009908745.1	s__Phaeodactylibacter sp009908745	75.2799	77	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Phaeodactylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698985.1	s__UBA6168 sp002698985	75.2764	50	3714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:23:58,989] [INFO] GTDB search result was written to GCF_002646595.1_ASM264659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:23:58,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:23:58,993] [INFO] DFAST_QC result json was written to GCF_002646595.1_ASM264659v1_genomic.fna/dqc_result.json
[2024-01-24 15:23:58,993] [INFO] DFAST_QC completed!
[2024-01-24 15:23:58,993] [INFO] Total running time: 0h4m10s