[2023-06-29 23:41:14,039] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:41:14,042] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:41:14,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference
[2023-06-29 23:41:15,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:41:15,351] [INFO] Task started: Prodigal
[2023-06-29 23:41:15,351] [INFO] Running command: gunzip -c /var/lib/cwl/stgd80e7d94-dc64-431a-8ced-c127812b372e/GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:41:32,842] [INFO] Task succeeded: Prodigal
[2023-06-29 23:41:32,842] [INFO] Task started: HMMsearch
[2023-06-29 23:41:32,842] [INFO] Running command: hmmsearch --tblout GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/reference_markers.hmm GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:41:33,093] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:41:33,095] [INFO] Found 6/6 markers.
[2023-06-29 23:41:33,123] [INFO] Query marker FASTA was written to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 23:41:33,123] [INFO] Task started: Blastn
[2023-06-29 23:41:33,123] [INFO] Running command: blastn -query GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/reference_markers.fasta -out GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:41:33,718] [INFO] Task succeeded: Blastn
[2023-06-29 23:41:33,723] [INFO] Selected 33 target genomes.
[2023-06-29 23:41:33,723] [INFO] Target genome list was writen to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 23:41:33,727] [INFO] Task started: fastANI
[2023-06-29 23:41:33,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80e7d94-dc64-431a-8ced-c127812b372e/GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:41:56,063] [INFO] Task succeeded: fastANI
[2023-06-29 23:41:56,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:41:56,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:41:56,065] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:41:56,066] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 23:41:56,066] [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
--------------------------------------------------------------------------------
[2023-06-29 23:41:56,068] [INFO] DFAST Taxonomy check result was written to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 23:41:56,069] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:41:56,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:41:56,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/checkm_data
[2023-06-29 23:41:56,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:41:56,104] [INFO] Task started: CheckM
[2023-06-29 23:41:56,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 23:42:48,127] [INFO] Task succeeded: CheckM
[2023-06-29 23:42:48,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:42:48,148] [INFO] ===== Completeness check finished =====
[2023-06-29 23:42:48,148] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:42:48,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 23:42:48,149] [INFO] Task started: Blastn
[2023-06-29 23:42:48,149] [INFO] Running command: blastn -query GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c24f17-167f-48d2-a079-b0f30d63250d/dqc_reference/reference_markers_gtdb.fasta -out GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:42:49,013] [INFO] Task succeeded: Blastn
[2023-06-29 23:42:49,018] [INFO] Selected 18 target genomes.
[2023-06-29 23:42:49,018] [INFO] Target genome list was writen to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:42:49,027] [INFO] Task started: fastANI
[2023-06-29 23:42:49,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgd80e7d94-dc64-431a-8ced-c127812b372e/GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:42:58,589] [INFO] Task succeeded: fastANI
[2023-06-29 23:42:58,607] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:42:58,607] [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_902789725.1	s__UBA4334 sp002363115	98.934	778	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.06	99.06	0.84	0.84	2	conclusive
GCA_002393555.1	s__UBA4334 sp002393555	79.8663	334	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.14	96.87	0.79	0.76	3	-
GCA_017470525.1	s__UBA4334 sp017470525	79.3924	405	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316975.1	s__UBA4334 sp900316975	79.3505	322	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.29	0.86	0.80	13	-
GCA_905234125.1	s__UBA4334 sp905234125	78.8932	328	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
GCA_902768125.1	s__UBA4334 sp902768125	78.8552	285	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_902801475.1	s__UBA4334 sp902801475	78.8531	296	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.71	97.36	0.83	0.79	15	-
GCA_017483605.1	s__UBA4334 sp017483605	78.8412	312	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
GCA_902800305.1	s__UBA4334 sp902800305	78.455	313	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.11	97.11	0.80	0.80	2	-
GCA_017651245.1	s__UBA4334 sp017651245	78.4264	299	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280445.1	s__UBA4334 sp016280445	78.424	332	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017448825.1	s__UBA4334 sp017448825	78.411	315	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318775.1	s__UBA4334 sp900318775	78.2736	255	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.63	98.03	0.91	0.87	6	-
GCA_904501945.1	s__UBA4334 sp904501945	77.6004	155	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018064885.1	s__UBA4334 sp018064885	76.7396	109	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534705.1	s__RUG11857 sp017534705	76.7047	63	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__RUG11857	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:42:58,609] [INFO] GTDB search result was written to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 23:42:58,610] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:42:58,613] [INFO] DFAST_QC result json was written to GCA_946413355.1_SRR12081294_bin.21_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 23:42:58,613] [INFO] DFAST_QC completed!
[2023-06-29 23:42:58,613] [INFO] Total running time: 0h1m45s