[2024-01-24 15:26:39,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference
[2024-01-24 15:26:41,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,105] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg26faad8f-43d2-4327-ac06-f0f78582fa5e/GCF_000428565.1_ASM42856v1_genomic.fna.gz | prodigal -d GCF_000428565.1_ASM42856v1_genomic.fna/cds.fna -a GCF_000428565.1_ASM42856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:11,978] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:11,978] [INFO] Task started: HMMsearch
[2024-01-24 15:27:11,979] [INFO] Running command: hmmsearch --tblout GCF_000428565.1_ASM42856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/reference_markers.hmm GCF_000428565.1_ASM42856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:12,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:12,343] [INFO] Found 6/6 markers.
[2024-01-24 15:27:12,396] [INFO] Query marker FASTA was written to GCF_000428565.1_ASM42856v1_genomic.fna/markers.fasta
[2024-01-24 15:27:12,397] [INFO] Task started: Blastn
[2024-01-24 15:27:12,397] [INFO] Running command: blastn -query GCF_000428565.1_ASM42856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/reference_markers.fasta -out GCF_000428565.1_ASM42856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:13,035] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:13,039] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:13,039] [INFO] Target genome list was writen to GCF_000428565.1_ASM42856v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:13,045] [INFO] Task started: fastANI
[2024-01-24 15:27:13,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg26faad8f-43d2-4327-ac06-f0f78582fa5e/GCF_000428565.1_ASM42856v1_genomic.fna.gz --refList GCF_000428565.1_ASM42856v1_genomic.fna/target_genomes.txt --output GCF_000428565.1_ASM42856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:31,209] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:31,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:31,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:31,222] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:27:31,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:31,223] [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
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	100.0	2197	2199	95	conclusive
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	99.9875	2197	2199	95	conclusive
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	99.9847	2197	2199	95	conclusive
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	84.744	1396	2199	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	83.6981	1191	2199	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	82.4867	1121	2199	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	82.3437	1135	2199	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	79.4245	594	2199	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.3008	156	2199	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.9579	491	2199	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.473	127	2199	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.4635	123	2199	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	76.9715	106	2199	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	76.5554	103	2199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:31,224] [INFO] DFAST Taxonomy check result was written to GCF_000428565.1_ASM42856v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:31,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:31,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:31,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/checkm_data
[2024-01-24 15:27:31,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:31,288] [INFO] Task started: CheckM
[2024-01-24 15:27:31,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428565.1_ASM42856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428565.1_ASM42856v1_genomic.fna/checkm_input GCF_000428565.1_ASM42856v1_genomic.fna/checkm_result
[2024-01-24 15:28:54,026] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:54,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:54,054] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:54,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:54,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428565.1_ASM42856v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:54,056] [INFO] Task started: Blastn
[2024-01-24 15:28:54,056] [INFO] Running command: blastn -query GCF_000428565.1_ASM42856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d007e47-82d9-4d7a-8e49-b412acd32145/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428565.1_ASM42856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:54,932] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:54,938] [INFO] Selected 9 target genomes.
[2024-01-24 15:28:54,938] [INFO] Target genome list was writen to GCF_000428565.1_ASM42856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:54,947] [INFO] Task started: fastANI
[2024-01-24 15:28:54,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg26faad8f-43d2-4327-ac06-f0f78582fa5e/GCF_000428565.1_ASM42856v1_genomic.fna.gz --refList GCF_000428565.1_ASM42856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428565.1_ASM42856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:06,931] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:06,942] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:06,942] [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_000969825.1	s__Parabacteroides gordonii	99.9847	2197	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	conclusive
GCA_905196875.1	s__Parabacteroides sp905196875	86.4506	1316	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550595.1	s__Parabacteroides sp900540715	85.3745	1378	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_900128505.1	s__Parabacteroides timonensis	84.7868	1388	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_000969835.1	s__Parabacteroides goldsteinii	83.6913	1192	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCF_003480915.1	s__Parabacteroides sp003480915	82.8658	1178	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_014647375.1	s__Parabacteroides faecis	82.3596	1132	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCF_003363715.1	s__Parabacteroides acidifaciens	79.4351	592	2199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:06,944] [INFO] GTDB search result was written to GCF_000428565.1_ASM42856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:06,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:06,947] [INFO] DFAST_QC result json was written to GCF_000428565.1_ASM42856v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:06,948] [INFO] DFAST_QC completed!
[2024-01-24 15:29:06,948] [INFO] Total running time: 0h2m27s