[2023-06-13 16:36:18,575] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:36:18,577] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:36:18,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference
[2023-06-13 16:36:19,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:36:19,785] [INFO] Task started: Prodigal
[2023-06-13 16:36:19,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg59a95474-d1d8-4e02-877d-cce054211682/GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:36:26,965] [INFO] Task succeeded: Prodigal
[2023-06-13 16:36:26,966] [INFO] Task started: HMMsearch
[2023-06-13 16:36:26,966] [INFO] Running command: hmmsearch --tblout GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/reference_markers.hmm GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:36:27,218] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:36:27,220] [INFO] Found 6/6 markers.
[2023-06-13 16:36:27,251] [INFO] Query marker FASTA was written to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 16:36:27,252] [INFO] Task started: Blastn
[2023-06-13 16:36:27,252] [INFO] Running command: blastn -query GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/reference_markers.fasta -out GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:27,826] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:27,830] [INFO] Selected 12 target genomes.
[2023-06-13 16:36:27,830] [INFO] Target genome list was writen to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 16:36:27,834] [INFO] Task started: fastANI
[2023-06-13 16:36:27,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a95474-d1d8-4e02-877d-cce054211682/GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:36:34,057] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:34,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:36:34,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:36:34,061] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:36:34,061] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 16:36:34,061] [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
--------------------------------------------------------------------------------
[2023-06-13 16:36:34,063] [INFO] DFAST Taxonomy check result was written to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 16:36:34,064] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:36:34,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:36:34,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/checkm_data
[2023-06-13 16:36:34,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:36:34,102] [INFO] Task started: CheckM
[2023-06-13 16:36:34,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 16:37:01,250] [INFO] Task succeeded: CheckM
[2023-06-13 16:37:01,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:37:01,270] [INFO] ===== Completeness check finished =====
[2023-06-13 16:37:01,271] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:37:01,271] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 16:37:01,271] [INFO] Task started: Blastn
[2023-06-13 16:37:01,272] [INFO] Running command: blastn -query GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg50816df0-8322-4d6b-873e-b99f0f4c5bfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:37:02,025] [INFO] Task succeeded: Blastn
[2023-06-13 16:37:02,030] [INFO] Selected 17 target genomes.
[2023-06-13 16:37:02,030] [INFO] Target genome list was writen to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:37:02,038] [INFO] Task started: fastANI
[2023-06-13 16:37:02,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a95474-d1d8-4e02-877d-cce054211682/GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:37:10,311] [INFO] Task succeeded: fastANI
[2023-06-13 16:37:10,324] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 16:37:10,325] [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_014804005.1	s__Treponema_D sp014804005	91.3805	567	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.90	95.85	0.85	0.84	4	-
GCA_910584475.1	s__Treponema_D sp910584475	84.9358	591	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804085.1	s__Treponema_D sp014804085	81.1305	115	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.34	95.30	0.82	0.78	3	-
GCA_902799965.1	s__Treponema_D sp902799965	77.2322	145	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792795.1	s__Treponema_D sp902792795	76.9188	140	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.12	97.12	0.85	0.85	2	-
GCA_900316905.1	s__Treponema_D sp900316905	76.6577	146	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.02	96.19	0.87	0.83	16	-
GCA_905233535.1	s__Treponema_D sp905233535	75.7415	55	831	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:37:10,327] [INFO] GTDB search result was written to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 16:37:10,328] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:37:10,331] [INFO] DFAST_QC result json was written to GCA_947178095.1_SRR14411325_bin.9_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 16:37:10,331] [INFO] DFAST_QC completed!
[2023-06-13 16:37:10,331] [INFO] Total running time: 0h0m52s