[2023-06-13 14:58:18,040] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:58:18,042] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:58:18,043] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference
[2023-06-13 14:58:19,196] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:58:19,197] [INFO] Task started: Prodigal
[2023-06-13 14:58:19,197] [INFO] Running command: gunzip -c /var/lib/cwl/stgaff94897-5def-4133-af3f-48cc206a9b76/GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:58:38,667] [INFO] Task succeeded: Prodigal
[2023-06-13 14:58:38,667] [INFO] Task started: HMMsearch
[2023-06-13 14:58:38,667] [INFO] Running command: hmmsearch --tblout GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/reference_markers.hmm GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:58:38,934] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:58:38,936] [INFO] Found 6/6 markers.
[2023-06-13 14:58:38,969] [INFO] Query marker FASTA was written to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:58:38,969] [INFO] Task started: Blastn
[2023-06-13 14:58:38,969] [INFO] Running command: blastn -query GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/reference_markers.fasta -out GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:58:39,599] [INFO] Task succeeded: Blastn
[2023-06-13 14:58:39,604] [INFO] Selected 27 target genomes.
[2023-06-13 14:58:39,604] [INFO] Target genome list was writen to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:58:39,606] [INFO] Task started: fastANI
[2023-06-13 14:58:39,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff94897-5def-4133-af3f-48cc206a9b76/GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:58:56,630] [INFO] Task succeeded: fastANI
[2023-06-13 14:58:56,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:58:56,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:58:56,651] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:58:56,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:58:56,652] [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
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	79.0355	348	1068	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.9902	353	1068	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.8466	321	1068	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.5543	309	1068	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	78.5106	326	1068	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	78.5071	331	1068	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.492	328	1068	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.4804	310	1068	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.4593	314	1068	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	78.4537	332	1068	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	78.4142	334	1068	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.389	284	1068	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	78.3708	269	1068	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	78.3509	270	1068	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.3443	283	1068	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.3064	272	1068	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.3064	315	1068	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.2357	165	1068	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	77.8937	162	1068	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	77.631	125	1068	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	77.6145	126	1068	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.5904	187	1068	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	77.3721	156	1068	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.3783	80	1068	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.338	81	1068	95	below_threshold
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	76.26	63	1068	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2251	80	1068	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:58:56,654] [INFO] DFAST Taxonomy check result was written to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:58:56,655] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:58:56,655] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:58:56,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/checkm_data
[2023-06-13 14:58:56,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:58:56,696] [INFO] Task started: CheckM
[2023-06-13 14:58:56,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:59:51,895] [INFO] Task succeeded: CheckM
[2023-06-13 14:59:51,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:59:51,920] [INFO] ===== Completeness check finished =====
[2023-06-13 14:59:51,920] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:59:51,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:59:51,921] [INFO] Task started: Blastn
[2023-06-13 14:59:51,921] [INFO] Running command: blastn -query GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe6007a0-39d5-49fd-b214-69e719213ee3/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:52,965] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:52,970] [INFO] Selected 12 target genomes.
[2023-06-13 14:59:52,970] [INFO] Target genome list was writen to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:59:52,972] [INFO] Task started: fastANI
[2023-06-13 14:59:52,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgaff94897-5def-4133-af3f-48cc206a9b76/GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:00:01,839] [INFO] Task succeeded: fastANI
[2023-06-13 15:00:01,854] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:00:01,854] [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_900128475.1	s__Bacteroides massiliensis	97.247	926	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	conclusive
GCA_019116805.1	s__Bacteroides merdavium	87.0762	620	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	85.7926	697	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900108345.1	s__Bacteroides ndongoniae	81.8618	525	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_905201685.1	s__Bacteroides sp905201685	80.7432	217	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553815.1	s__Bacteroides sp900553815	80.0776	352	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_019116285.1	s__Bacteroides merdigallinarum	79.5941	316	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471925.1	s__Bacteroides sp017471925	79.0598	347	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	79.0291	295	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160055.1	s__Bacteroides avicola	78.6138	308	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.46	98.46	0.91	0.91	2	-
GCF_000154525.1	s__Bacteroides stercoris	78.4475	315	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.3311	264	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-13 15:00:01,856] [INFO] GTDB search result was written to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 15:00:01,856] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:00:01,861] [INFO] DFAST_QC result json was written to GCA_938048375.1_ERR414334_bin.55_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 15:00:01,861] [INFO] DFAST_QC completed!
[2023-06-13 15:00:01,861] [INFO] Total running time: 0h1m44s