[2023-06-08 12:18:51,167] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:18:51,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:18:51,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference
[2023-06-08 12:18:52,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:18:52,479] [INFO] Task started: Prodigal
[2023-06-08 12:18:52,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c7c7134-0c5b-4bf4-bfef-9234609cf66c/GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:19:08,711] [INFO] Task succeeded: Prodigal
[2023-06-08 12:19:08,712] [INFO] Task started: HMMsearch
[2023-06-08 12:19:08,712] [INFO] Running command: hmmsearch --tblout GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/reference_markers.hmm GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:19:08,911] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:19:08,912] [INFO] Found 6/6 markers.
[2023-06-08 12:19:08,935] [INFO] Query marker FASTA was written to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:19:08,935] [INFO] Task started: Blastn
[2023-06-08 12:19:08,935] [INFO] Running command: blastn -query GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/reference_markers.fasta -out GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:09,503] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:09,507] [INFO] Selected 30 target genomes.
[2023-06-08 12:19:09,507] [INFO] Target genome list was writen to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:19:09,508] [INFO] Task started: fastANI
[2023-06-08 12:19:09,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7c7134-0c5b-4bf4-bfef-9234609cf66c/GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:19:23,712] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:23,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:19:23,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:19:23,717] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:19:23,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:19:23,717] [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
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.5375	57	706	95	below_threshold
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	76.439	51	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:19:23,719] [INFO] DFAST Taxonomy check result was written to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:19:23,720] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:19:23,720] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:19:23,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/checkm_data
[2023-06-08 12:19:23,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:19:23,749] [INFO] Task started: CheckM
[2023-06-08 12:19:23,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:20:10,275] [INFO] Task succeeded: CheckM
[2023-06-08 12:20:10,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 12:20:10,295] [INFO] ===== Completeness check finished =====
[2023-06-08 12:20:10,295] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:20:10,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:20:10,296] [INFO] Task started: Blastn
[2023-06-08 12:20:10,296] [INFO] Running command: blastn -query GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ebbf1a-1d0f-40f0-b3fa-887d1dcd5ef0/dqc_reference/reference_markers_gtdb.fasta -out GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:20:11,147] [INFO] Task succeeded: Blastn
[2023-06-08 12:20:11,150] [INFO] Selected 24 target genomes.
[2023-06-08 12:20:11,151] [INFO] Target genome list was writen to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:20:11,157] [INFO] Task started: fastANI
[2023-06-08 12:20:11,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7c7134-0c5b-4bf4-bfef-9234609cf66c/GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:20:22,128] [INFO] Task succeeded: fastANI
[2023-06-08 12:20:22,144] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:20:22,144] [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_016292545.1	s__UBA4372 sp016292545	86.0905	500	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543815.1	s__UBA4372 sp900543815	77.9693	184	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
GCA_017379075.1	s__UBA4372 sp017379075	77.8347	189	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_017559845.1	s__UBA4372 sp017559845	77.7559	183	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788315.1	s__UBA4372 sp902788315	77.6559	155	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.21	97.94	0.89	0.88	4	-
GCA_017935785.1	s__UBA4372 sp017935785	77.6175	184	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.67	97.67	0.84	0.84	2	-
GCA_900320435.1	s__UBA4372 sp900320435	77.4527	96	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	-
GCA_002394305.1	s__UBA4372 sp002394305	77.3693	157	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_902783655.1	s__UBA4372 sp902783655	77.1928	91	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775385.1	s__UBA4372 sp902775385	77.1569	104	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.32	98.32	0.92	0.92	2	-
GCA_017524545.1	s__UBA4372 sp017524545	77.1283	168	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787575.1	s__UBA4372 sp900320715	76.9423	120	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.55	98.27	0.96	0.94	8	-
GCA_017464815.1	s__Phocaeicola_A sp017464815	76.8771	75	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280855.1	s__UBA4372 sp016280855	76.8462	75	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317475.1	s__UBA4372 sp002317475	76.8408	57	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.595	75	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000205165.1	s__Paraprevotella xylaniphila	76.439	51	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.99	98.53	0.93	0.88	5	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	76.3957	59	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
GCA_017524385.1	s__Prevotella sp017524385	76.3746	59	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548345.1	s__Paraprevotella sp900548345	76.3745	59	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-08 12:20:22,146] [INFO] GTDB search result was written to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:20:22,147] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:20:22,150] [INFO] DFAST_QC result json was written to GCA_945638405.1_SRR14474051_bin.16_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:20:22,151] [INFO] DFAST_QC completed!
[2023-06-08 12:20:22,151] [INFO] Total running time: 0h1m31s