[2023-06-30 02:23:07,079] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:23:07,081] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:23:07,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference
[2023-06-30 02:23:08,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:23:08,381] [INFO] Task started: Prodigal
[2023-06-30 02:23:08,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg91897743-7f22-42a0-b3e8-44cb2dad1904/GCA_900762435.1_SRS143342_30_genomic.fna.gz | prodigal -d GCA_900762435.1_SRS143342_30_genomic.fna/cds.fna -a GCA_900762435.1_SRS143342_30_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:23:23,937] [INFO] Task succeeded: Prodigal
[2023-06-30 02:23:23,938] [INFO] Task started: HMMsearch
[2023-06-30 02:23:23,938] [INFO] Running command: hmmsearch --tblout GCA_900762435.1_SRS143342_30_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/reference_markers.hmm GCA_900762435.1_SRS143342_30_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:23:24,201] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:23:24,203] [INFO] Found 6/6 markers.
[2023-06-30 02:23:24,232] [INFO] Query marker FASTA was written to GCA_900762435.1_SRS143342_30_genomic.fna/markers.fasta
[2023-06-30 02:23:24,233] [INFO] Task started: Blastn
[2023-06-30 02:23:24,233] [INFO] Running command: blastn -query GCA_900762435.1_SRS143342_30_genomic.fna/markers.fasta -db /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/reference_markers.fasta -out GCA_900762435.1_SRS143342_30_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:23:24,857] [INFO] Task succeeded: Blastn
[2023-06-30 02:23:24,861] [INFO] Selected 26 target genomes.
[2023-06-30 02:23:24,861] [INFO] Target genome list was writen to GCA_900762435.1_SRS143342_30_genomic.fna/target_genomes.txt
[2023-06-30 02:23:24,862] [INFO] Task started: fastANI
[2023-06-30 02:23:24,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg91897743-7f22-42a0-b3e8-44cb2dad1904/GCA_900762435.1_SRS143342_30_genomic.fna.gz --refList GCA_900762435.1_SRS143342_30_genomic.fna/target_genomes.txt --output GCA_900762435.1_SRS143342_30_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:23:40,596] [INFO] Task succeeded: fastANI
[2023-06-30 02:23:40,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:23:40,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:23:40,612] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 02:23:40,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 02:23:40,612] [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
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.3495	73	874	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	77.9609	68	874	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	77.9438	68	874	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	77.4398	58	874	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	77.4224	59	874	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.2392	59	874	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	76.7075	52	874	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	76.586	51	874	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	76.5788	53	874	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 02:23:40,616] [INFO] DFAST Taxonomy check result was written to GCA_900762435.1_SRS143342_30_genomic.fna/tc_result.tsv
[2023-06-30 02:23:40,617] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:23:40,617] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:23:40,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/checkm_data
[2023-06-30 02:23:40,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:23:40,651] [INFO] Task started: CheckM
[2023-06-30 02:23:40,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900762435.1_SRS143342_30_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900762435.1_SRS143342_30_genomic.fna/checkm_input GCA_900762435.1_SRS143342_30_genomic.fna/checkm_result
[2023-06-30 02:24:27,730] [INFO] Task succeeded: CheckM
[2023-06-30 02:24:27,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 02:24:27,755] [INFO] ===== Completeness check finished =====
[2023-06-30 02:24:27,755] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:24:27,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900762435.1_SRS143342_30_genomic.fna/markers.fasta)
[2023-06-30 02:24:27,756] [INFO] Task started: Blastn
[2023-06-30 02:24:27,756] [INFO] Running command: blastn -query GCA_900762435.1_SRS143342_30_genomic.fna/markers.fasta -db /var/lib/cwl/stg90014283-3e7d-4b50-ba4e-d91e055705b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_900762435.1_SRS143342_30_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:24:28,625] [INFO] Task succeeded: Blastn
[2023-06-30 02:24:28,630] [INFO] Selected 19 target genomes.
[2023-06-30 02:24:28,630] [INFO] Target genome list was writen to GCA_900762435.1_SRS143342_30_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:24:28,639] [INFO] Task started: fastANI
[2023-06-30 02:24:28,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg91897743-7f22-42a0-b3e8-44cb2dad1904/GCA_900762435.1_SRS143342_30_genomic.fna.gz --refList GCA_900762435.1_SRS143342_30_genomic.fna/target_genomes_gtdb.txt --output GCA_900762435.1_SRS143342_30_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:24:37,581] [INFO] Task succeeded: fastANI
[2023-06-30 02:24:37,594] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:24:37,595] [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
GCA_900544305.1	s__Limisoma sp900544305	97.9556	779	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	97.92	97.84	0.88	0.86	3	conclusive
GCA_900548875.1	s__Limisoma sp900548875	88.8182	698	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	97.13	97.13	0.85	0.85	2	-
GCA_900541935.1	s__Limisoma sp900541935	77.974	85	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.32	96.63	0.93	0.87	3	-
GCA_000437795.1	s__Limisoma sp000437795	77.8008	141	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.05	97.80	0.87	0.76	12	-
GCA_017694955.1	s__Limisoma faecipullorum	77.6737	100	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555955.1	s__Limisoma sp004555955	77.6057	105	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157915.1	s__Phocaeicola coprophilus	77.4398	58	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_900550025.1	s__Limisoma gallistercoris	77.0699	95	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.17	98.10	0.82	0.79	4	-
GCA_900541555.1	s__Limisoma intestinavium	77.0382	81	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Limisoma	95.0	98.58	98.56	0.93	0.91	3	-
GCA_900538555.1	s__UMGS27 sp900538555	76.494	66	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
GCA_905207705.1	s__Avimuribaculum sp905207705	76.038	51	874	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Avimuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 02:24:37,597] [INFO] GTDB search result was written to GCA_900762435.1_SRS143342_30_genomic.fna/result_gtdb.tsv
[2023-06-30 02:24:37,597] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:24:37,601] [INFO] DFAST_QC result json was written to GCA_900762435.1_SRS143342_30_genomic.fna/dqc_result.json
[2023-06-30 02:24:37,601] [INFO] DFAST_QC completed!
[2023-06-30 02:24:37,601] [INFO] Total running time: 0h1m31s