[2023-06-13 01:40:16,127] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:40:16,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:40:16,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference
[2023-06-13 01:40:17,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:40:17,341] [INFO] Task started: Prodigal
[2023-06-13 01:40:17,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgef0cc857-5d64-484c-a972-63583bf358a2/GCA_022720775.1_ASM2272077v1_genomic.fna.gz | prodigal -d GCA_022720775.1_ASM2272077v1_genomic.fna/cds.fna -a GCA_022720775.1_ASM2272077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:40:41,720] [INFO] Task succeeded: Prodigal
[2023-06-13 01:40:41,720] [INFO] Task started: HMMsearch
[2023-06-13 01:40:41,720] [INFO] Running command: hmmsearch --tblout GCA_022720775.1_ASM2272077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/reference_markers.hmm GCA_022720775.1_ASM2272077v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:40:42,012] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:40:42,014] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgef0cc857-5d64-484c-a972-63583bf358a2/GCA_022720775.1_ASM2272077v1_genomic.fna.gz]
[2023-06-13 01:40:42,057] [INFO] Query marker FASTA was written to GCA_022720775.1_ASM2272077v1_genomic.fna/markers.fasta
[2023-06-13 01:40:42,057] [INFO] Task started: Blastn
[2023-06-13 01:40:42,057] [INFO] Running command: blastn -query GCA_022720775.1_ASM2272077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/reference_markers.fasta -out GCA_022720775.1_ASM2272077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:42,647] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:42,652] [INFO] Selected 9 target genomes.
[2023-06-13 01:40:42,652] [INFO] Target genome list was writen to GCA_022720775.1_ASM2272077v1_genomic.fna/target_genomes.txt
[2023-06-13 01:40:42,654] [INFO] Task started: fastANI
[2023-06-13 01:40:42,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0cc857-5d64-484c-a972-63583bf358a2/GCA_022720775.1_ASM2272077v1_genomic.fna.gz --refList GCA_022720775.1_ASM2272077v1_genomic.fna/target_genomes.txt --output GCA_022720775.1_ASM2272077v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:40:51,759] [INFO] Task succeeded: fastANI
[2023-06-13 01:40:51,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:40:51,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:40:51,772] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 01:40:51,772] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-13 01:40:51,773] [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 vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	98.8175	1221	1540	95	inconclusive
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	98.8114	1224	1540	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	95.4341	1214	1540	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	95.3924	1227	1540	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	95.3716	1228	1540	95	inconclusive
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	90.402	1031	1540	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	80.703	201	1540	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.1288	216	1540	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.8491	186	1540	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:40:51,775] [INFO] DFAST Taxonomy check result was written to GCA_022720775.1_ASM2272077v1_genomic.fna/tc_result.tsv
[2023-06-13 01:40:51,775] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:40:51,775] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:40:51,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/checkm_data
[2023-06-13 01:40:51,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:40:51,826] [INFO] Task started: CheckM
[2023-06-13 01:40:51,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720775.1_ASM2272077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720775.1_ASM2272077v1_genomic.fna/checkm_input GCA_022720775.1_ASM2272077v1_genomic.fna/checkm_result
[2023-06-13 01:42:00,038] [INFO] Task succeeded: CheckM
[2023-06-13 01:42:00,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:42:00,065] [INFO] ===== Completeness check finished =====
[2023-06-13 01:42:00,066] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:42:00,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720775.1_ASM2272077v1_genomic.fna/markers.fasta)
[2023-06-13 01:42:00,067] [INFO] Task started: Blastn
[2023-06-13 01:42:00,067] [INFO] Running command: blastn -query GCA_022720775.1_ASM2272077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2452659b-b150-4ae3-a3cf-7d95213e61a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720775.1_ASM2272077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:42:00,880] [INFO] Task succeeded: Blastn
[2023-06-13 01:42:00,887] [INFO] Selected 7 target genomes.
[2023-06-13 01:42:00,887] [INFO] Target genome list was writen to GCA_022720775.1_ASM2272077v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:42:00,894] [INFO] Task started: fastANI
[2023-06-13 01:42:00,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0cc857-5d64-484c-a972-63583bf358a2/GCA_022720775.1_ASM2272077v1_genomic.fna.gz --refList GCA_022720775.1_ASM2272077v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720775.1_ASM2272077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:42:08,436] [INFO] Task succeeded: fastANI
[2023-06-13 01:42:08,450] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 01:42:08,451] [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_000012825.1	s__Phocaeicola vulgatus	98.8114	1224	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	inconclusive
GCF_013009555.1	s__Phocaeicola dorei	95.4169	1215	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	inconclusive
GCA_900760795.1	s__Phocaeicola sp900760795	93.9856	800	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614185.1	s__Phocaeicola sartorii	90.3888	1021	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_011959205.1	s__Phocaeicola sp011959205	90.2037	787	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000382445.1	s__Phocaeicola massiliensis	83.1849	620	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCA_902388365.1	s__Phocaeicola sp902388365	81.3833	788	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-13 01:42:08,455] [INFO] GTDB search result was written to GCA_022720775.1_ASM2272077v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:42:08,456] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:42:08,460] [INFO] DFAST_QC result json was written to GCA_022720775.1_ASM2272077v1_genomic.fna/dqc_result.json
[2023-06-13 01:42:08,460] [INFO] DFAST_QC completed!
[2023-06-13 01:42:08,461] [INFO] Total running time: 0h1m52s