[2024-01-24 14:12:35,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference
[2024-01-24 14:12:36,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:36,612] [INFO] Task started: Prodigal
[2024-01-24 14:12:36,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg54c81545-d6e8-4b62-ad4c-2f0506a18540/GCF_900292045.1_PRJEB24955_genomic.fna.gz | prodigal -d GCF_900292045.1_PRJEB24955_genomic.fna/cds.fna -a GCF_900292045.1_PRJEB24955_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:59,235] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:59,236] [INFO] Task started: HMMsearch
[2024-01-24 14:12:59,236] [INFO] Running command: hmmsearch --tblout GCF_900292045.1_PRJEB24955_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/reference_markers.hmm GCF_900292045.1_PRJEB24955_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:59,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:59,555] [INFO] Found 6/6 markers.
[2024-01-24 14:12:59,598] [INFO] Query marker FASTA was written to GCF_900292045.1_PRJEB24955_genomic.fna/markers.fasta
[2024-01-24 14:12:59,598] [INFO] Task started: Blastn
[2024-01-24 14:12:59,598] [INFO] Running command: blastn -query GCF_900292045.1_PRJEB24955_genomic.fna/markers.fasta -db /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/reference_markers.fasta -out GCF_900292045.1_PRJEB24955_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:00,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:00,261] [INFO] Selected 25 target genomes.
[2024-01-24 14:13:00,261] [INFO] Target genome list was writen to GCF_900292045.1_PRJEB24955_genomic.fna/target_genomes.txt
[2024-01-24 14:13:00,279] [INFO] Task started: fastANI
[2024-01-24 14:13:00,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c81545-d6e8-4b62-ad4c-2f0506a18540/GCF_900292045.1_PRJEB24955_genomic.fna.gz --refList GCF_900292045.1_PRJEB24955_genomic.fna/target_genomes.txt --output GCF_900292045.1_PRJEB24955_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:19,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:19,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:19,470] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:19,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:19,470] [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 pacaensis	strain=Marseille-P4001	GCA_900292045.1	2086575	2086575	type	True	100.0	1739	1741	95	conclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	78.8008	131	1741	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	78.679	70	1741	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	78.5163	146	1741	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	78.3307	147	1741	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.1805	135	1741	95	below_threshold
Parabacteroides bouchesdurhonensis	strain=Marseille-P3763	GCA_900186615.1	1936995	1936995	type	True	78.1092	171	1741	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	78.0513	143	1741	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	78.032	54	1741	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	78.0121	132	1741	95	below_threshold
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	77.9705	66	1741	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.9271	151	1741	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	77.9074	80	1741	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	77.8147	143	1741	95	below_threshold
Bacteroides cutis	strain=Marseille-P4118	GCA_900241005.1	2024197	2024197	type	True	77.6436	62	1741	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	77.024	59	1741	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.0178	62	1741	95	below_threshold
Bacteroides reticulotermitis	strain=DSM 105720	GCA_014196955.1	1133319	1133319	type	True	76.7897	52	1741	95	below_threshold
Bacteroides reticulotermitis	strain=JCM 10512	GCA_000517545.1	1133319	1133319	type	True	76.6099	50	1741	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,472] [INFO] DFAST Taxonomy check result was written to GCF_900292045.1_PRJEB24955_genomic.fna/tc_result.tsv
[2024-01-24 14:13:19,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:19,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:19,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/checkm_data
[2024-01-24 14:13:19,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:19,531] [INFO] Task started: CheckM
[2024-01-24 14:13:19,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900292045.1_PRJEB24955_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900292045.1_PRJEB24955_genomic.fna/checkm_input GCF_900292045.1_PRJEB24955_genomic.fna/checkm_result
[2024-01-24 14:14:18,644] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:18,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:18,667] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:18,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:18,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900292045.1_PRJEB24955_genomic.fna/markers.fasta)
[2024-01-24 14:14:18,668] [INFO] Task started: Blastn
[2024-01-24 14:14:18,669] [INFO] Running command: blastn -query GCF_900292045.1_PRJEB24955_genomic.fna/markers.fasta -db /var/lib/cwl/stg37701273-f05f-4894-bc99-e4978d7714be/dqc_reference/reference_markers_gtdb.fasta -out GCF_900292045.1_PRJEB24955_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:19,533] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:19,538] [INFO] Selected 27 target genomes.
[2024-01-24 14:14:19,538] [INFO] Target genome list was writen to GCF_900292045.1_PRJEB24955_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:19,646] [INFO] Task started: fastANI
[2024-01-24 14:14:19,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c81545-d6e8-4b62-ad4c-2f0506a18540/GCF_900292045.1_PRJEB24955_genomic.fna.gz --refList GCF_900292045.1_PRJEB24955_genomic.fna/target_genomes_gtdb.txt --output GCF_900292045.1_PRJEB24955_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:37,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:37,095] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:37,095] [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_900292045.1	s__Parabacteroides_B pacaensis	100.0	1740	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000969825.1	s__Parabacteroides gordonii	78.581	146	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_000186225.1	s__Bacteroides helcogenes	78.3267	52	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186615.1	s__Parabacteroides bouchesdurhonensis	78.1252	169	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.72	97.72	0.92	0.92	3	-
GCF_900128505.1	s__Parabacteroides timonensis	78.0256	141	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
GCF_003473295.1	s__Parabacteroides sp003473295	77.9785	188	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.9752	135	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_900155425.1	s__Parabacteroides massiliensis	77.9744	124	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCF_014287585.1	s__Parabacteroides sp014287585	77.9645	132	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCF_000969835.1	s__Parabacteroides goldsteinii	77.9358	150	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
GCA_017481945.1	s__Parabacteroides sp017481945	77.8466	89	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.47	98.47	0.80	0.80	2	-
GCF_900108035.1	s__Parabacteroides chinchillae	77.8007	147	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.95	97.95	0.87	0.87	3	-
GCA_910577325.1	s__Parabacteroides sp910577325	77.7994	110	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060925.1	s__Parabacteroides distasonis_B	77.3091	102	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.66	98.66	0.86	0.86	2	-
GCA_905196875.1	s__Parabacteroides sp905196875	77.0605	143	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548175.1	s__Parabacteroides sp900548175	76.9961	67	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.23	96.23	0.78	0.78	2	-
GCA_905215345.1	s__Bacteroides sp905215345	76.5298	69	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500995.1	s__Bacteroides_H sp010500995	76.4986	60	1741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_H	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:37,097] [INFO] GTDB search result was written to GCF_900292045.1_PRJEB24955_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:37,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:37,101] [INFO] DFAST_QC result json was written to GCF_900292045.1_PRJEB24955_genomic.fna/dqc_result.json
[2024-01-24 14:14:37,101] [INFO] DFAST_QC completed!
[2024-01-24 14:14:37,102] [INFO] Total running time: 0h2m2s