[2023-06-28 04:37:05,065] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:37:05,075] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:37:05,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference
[2023-06-28 04:37:06,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:06,403] [INFO] Task started: Prodigal
[2023-06-28 04:37:06,403] [INFO] Running command: gunzip -c /var/lib/cwl/stg66f2c4a3-035e-4d53-a199-642182f86843/GCA_944321565.1_BRZ_KA_bin9_genomic.fna.gz | prodigal -d GCA_944321565.1_BRZ_KA_bin9_genomic.fna/cds.fna -a GCA_944321565.1_BRZ_KA_bin9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:28,074] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:28,074] [INFO] Task started: HMMsearch
[2023-06-28 04:37:28,075] [INFO] Running command: hmmsearch --tblout GCA_944321565.1_BRZ_KA_bin9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/reference_markers.hmm GCA_944321565.1_BRZ_KA_bin9_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:28,328] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:28,329] [INFO] Found 6/6 markers.
[2023-06-28 04:37:28,357] [INFO] Query marker FASTA was written to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/markers.fasta
[2023-06-28 04:37:28,357] [INFO] Task started: Blastn
[2023-06-28 04:37:28,358] [INFO] Running command: blastn -query GCA_944321565.1_BRZ_KA_bin9_genomic.fna/markers.fasta -db /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/reference_markers.fasta -out GCA_944321565.1_BRZ_KA_bin9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:29,027] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:29,031] [INFO] Selected 24 target genomes.
[2023-06-28 04:37:29,032] [INFO] Target genome list was writen to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/target_genomes.txt
[2023-06-28 04:37:29,033] [INFO] Task started: fastANI
[2023-06-28 04:37:29,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f2c4a3-035e-4d53-a199-642182f86843/GCA_944321565.1_BRZ_KA_bin9_genomic.fna.gz --refList GCA_944321565.1_BRZ_KA_bin9_genomic.fna/target_genomes.txt --output GCA_944321565.1_BRZ_KA_bin9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:43,908] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:43,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:43,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:43,924] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:37:43,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:37:43,925] [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
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	78.5215	352	962	95	below_threshold
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	78.4062	359	962	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.2195	105	962	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.1385	95	962	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	76.8231	60	962	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	76.7607	60	962	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	76.7607	60	962	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	76.6376	57	962	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	76.5208	53	962	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4833	56	962	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	76.4061	51	962	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	76.1856	53	962	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	76.1579	65	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:37:43,927] [INFO] DFAST Taxonomy check result was written to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/tc_result.tsv
[2023-06-28 04:37:43,927] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:43,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:43,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/checkm_data
[2023-06-28 04:37:43,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:43,959] [INFO] Task started: CheckM
[2023-06-28 04:37:43,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321565.1_BRZ_KA_bin9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321565.1_BRZ_KA_bin9_genomic.fna/checkm_input GCA_944321565.1_BRZ_KA_bin9_genomic.fna/checkm_result
[2023-06-28 04:38:42,750] [INFO] Task succeeded: CheckM
[2023-06-28 04:38:42,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:38:42,773] [INFO] ===== Completeness check finished =====
[2023-06-28 04:38:42,773] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:38:42,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321565.1_BRZ_KA_bin9_genomic.fna/markers.fasta)
[2023-06-28 04:38:42,774] [INFO] Task started: Blastn
[2023-06-28 04:38:42,774] [INFO] Running command: blastn -query GCA_944321565.1_BRZ_KA_bin9_genomic.fna/markers.fasta -db /var/lib/cwl/stg031ba9d7-18ee-41b9-b777-364e970e7b2c/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321565.1_BRZ_KA_bin9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:38:43,622] [INFO] Task succeeded: Blastn
[2023-06-28 04:38:43,625] [INFO] Selected 26 target genomes.
[2023-06-28 04:38:43,626] [INFO] Target genome list was writen to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:38:43,666] [INFO] Task started: fastANI
[2023-06-28 04:38:43,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f2c4a3-035e-4d53-a199-642182f86843/GCA_944321565.1_BRZ_KA_bin9_genomic.fna.gz --refList GCA_944321565.1_BRZ_KA_bin9_genomic.fna/target_genomes_gtdb.txt --output GCA_944321565.1_BRZ_KA_bin9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:38:55,886] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:55,907] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:38:55,908] [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_000205165.1	s__Paraprevotella xylaniphila	78.5215	352	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.99	98.53	0.93	0.88	5	-
GCF_000233955.1	s__Paraprevotella clara	78.4062	359	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	97.73	97.27	0.87	0.80	9	-
GCA_910586505.1	s__Paraprevotella sp910586505	77.6165	199	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548345.1	s__Paraprevotella sp900548345	77.4463	224	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900760455.1	s__Paraprevotella sp900760455	77.2687	132	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
GCA_900546665.1	s__Paraprevotella stercorigallinarum	77.2093	111	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	99.24	99.20	0.80	0.74	3	-
GCA_018883665.1	s__Paraprevotella stercoravium	76.8719	84	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584955.1	s__Paraprevotella sp910584955	76.8249	114	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477995.1	s__Paraprevotella sp003477995	76.8203	125	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.53	97.92	0.95	0.91	5	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.7844	92	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	76.7192	108	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374585.1	s__Phocaeicola barnesiae	76.7001	74	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_003437535.1	s__Phocaeicola plebeius_A	76.6511	65	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCA_900546095.1	s__Phocaeicola excrementipullorum	76.5908	61	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.76	98.76	0.83	0.83	2	-
GCF_003438615.1	s__Bacteroides sp003545565	76.5064	50	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCA_017471925.1	s__Bacteroides sp017471925	76.4341	122	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215575.1	s__Paraprevotella sp905215575	76.2944	51	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316015.1	s__UBA4372 sp002316015	76.202	79	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	99.56	99.28	0.95	0.93	7	-
GCA_905214795.1	s__Paraprevotella sp905214795	76.1095	74	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187895.1	s__Phocaeicola plebeius	76.0414	65	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
--------------------------------------------------------------------------------
[2023-06-28 04:38:55,910] [INFO] GTDB search result was written to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/result_gtdb.tsv
[2023-06-28 04:38:55,910] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:38:55,915] [INFO] DFAST_QC result json was written to GCA_944321565.1_BRZ_KA_bin9_genomic.fna/dqc_result.json
[2023-06-28 04:38:55,915] [INFO] DFAST_QC completed!
[2023-06-28 04:38:55,915] [INFO] Total running time: 0h1m51s