[2023-06-08 10:53:07,922] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:53:07,925] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:53:07,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference
[2023-06-08 10:53:09,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:53:09,210] [INFO] Task started: Prodigal
[2023-06-08 10:53:09,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg946426b1-dce5-48e6-8585-60d146330d85/GCA_947491925.1_ZE-17mar17-80_genomic.fna.gz | prodigal -d GCA_947491925.1_ZE-17mar17-80_genomic.fna/cds.fna -a GCA_947491925.1_ZE-17mar17-80_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:53:20,379] [INFO] Task succeeded: Prodigal
[2023-06-08 10:53:20,380] [INFO] Task started: HMMsearch
[2023-06-08 10:53:20,380] [INFO] Running command: hmmsearch --tblout GCA_947491925.1_ZE-17mar17-80_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/reference_markers.hmm GCA_947491925.1_ZE-17mar17-80_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:53:20,652] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:53:20,654] [INFO] Found 6/6 markers.
[2023-06-08 10:53:20,684] [INFO] Query marker FASTA was written to GCA_947491925.1_ZE-17mar17-80_genomic.fna/markers.fasta
[2023-06-08 10:53:20,685] [INFO] Task started: Blastn
[2023-06-08 10:53:20,685] [INFO] Running command: blastn -query GCA_947491925.1_ZE-17mar17-80_genomic.fna/markers.fasta -db /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/reference_markers.fasta -out GCA_947491925.1_ZE-17mar17-80_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:53:21,299] [INFO] Task succeeded: Blastn
[2023-06-08 10:53:21,304] [INFO] Selected 22 target genomes.
[2023-06-08 10:53:21,305] [INFO] Target genome list was writen to GCA_947491925.1_ZE-17mar17-80_genomic.fna/target_genomes.txt
[2023-06-08 10:53:21,312] [INFO] Task started: fastANI
[2023-06-08 10:53:21,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg946426b1-dce5-48e6-8585-60d146330d85/GCA_947491925.1_ZE-17mar17-80_genomic.fna.gz --refList GCA_947491925.1_ZE-17mar17-80_genomic.fna/target_genomes.txt --output GCA_947491925.1_ZE-17mar17-80_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:53:36,715] [INFO] Task succeeded: fastANI
[2023-06-08 10:53:36,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:53:36,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:53:36,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:53:36,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:53:36,719] [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
--------------------------------------------------------------------------------
[2023-06-08 10:53:36,721] [INFO] DFAST Taxonomy check result was written to GCA_947491925.1_ZE-17mar17-80_genomic.fna/tc_result.tsv
[2023-06-08 10:53:36,721] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:53:36,721] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:53:36,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/checkm_data
[2023-06-08 10:53:36,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:53:36,767] [INFO] Task started: CheckM
[2023-06-08 10:53:36,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947491925.1_ZE-17mar17-80_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947491925.1_ZE-17mar17-80_genomic.fna/checkm_input GCA_947491925.1_ZE-17mar17-80_genomic.fna/checkm_result
[2023-06-08 10:54:19,152] [INFO] Task succeeded: CheckM
[2023-06-08 10:54:19,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:54:19,175] [INFO] ===== Completeness check finished =====
[2023-06-08 10:54:19,175] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:54:19,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947491925.1_ZE-17mar17-80_genomic.fna/markers.fasta)
[2023-06-08 10:54:19,176] [INFO] Task started: Blastn
[2023-06-08 10:54:19,176] [INFO] Running command: blastn -query GCA_947491925.1_ZE-17mar17-80_genomic.fna/markers.fasta -db /var/lib/cwl/stg000696db-da73-460a-988e-b96c71c09a20/dqc_reference/reference_markers_gtdb.fasta -out GCA_947491925.1_ZE-17mar17-80_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:54:19,992] [INFO] Task succeeded: Blastn
[2023-06-08 10:54:19,997] [INFO] Selected 10 target genomes.
[2023-06-08 10:54:19,997] [INFO] Target genome list was writen to GCA_947491925.1_ZE-17mar17-80_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:54:20,002] [INFO] Task started: fastANI
[2023-06-08 10:54:20,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg946426b1-dce5-48e6-8585-60d146330d85/GCA_947491925.1_ZE-17mar17-80_genomic.fna.gz --refList GCA_947491925.1_ZE-17mar17-80_genomic.fna/target_genomes_gtdb.txt --output GCA_947491925.1_ZE-17mar17-80_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:54:26,326] [INFO] Task succeeded: fastANI
[2023-06-08 10:54:26,340] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:54:26,340] [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_003671025.1	s__QWPT01 sp003671025	99.6223	943	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.38	99.11	0.93	0.92	3	conclusive
GCA_003671065.1	s__QWPT01 sp003671065	78.6117	269	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	97.91	97.83	0.77	0.73	3	-
GCA_003671055.1	s__F1-140-MAGs142 sp003671055	77.3611	155	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	99.26	99.00	0.90	0.89	3	-
GCA_003671075.1	s__QWPT01 sp003671075	77.3509	297	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	98.44	97.81	0.89	0.84	6	-
GCA_903891095.1	s__QWPT01 sp903891095	77.0587	312	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
GCA_016124975.1	s__QWPT01 sp016124975	77.0145	196	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911205.1	s__QWPT01 sp903911205	76.8386	202	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691805.1	s__F1-140-MAGs142 sp009691805	76.7858	142	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-140-MAGs142	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856525.1	s__QWPT01 sp903856525	76.7256	166	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	98.62	98.08	0.80	0.79	4	-
GCA_903918555.1	s__QWPT01 sp903918555	76.453	152	989	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:54:26,343] [INFO] GTDB search result was written to GCA_947491925.1_ZE-17mar17-80_genomic.fna/result_gtdb.tsv
[2023-06-08 10:54:26,343] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:54:26,346] [INFO] DFAST_QC result json was written to GCA_947491925.1_ZE-17mar17-80_genomic.fna/dqc_result.json
[2023-06-08 10:54:26,346] [INFO] DFAST_QC completed!
[2023-06-08 10:54:26,346] [INFO] Total running time: 0h1m18s