[2023-06-08 14:46:48,497] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:48,502] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:48,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference
[2023-06-08 14:46:50,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:50,053] [INFO] Task started: Prodigal
[2023-06-08 14:46:50,053] [INFO] Running command: gunzip -c /var/lib/cwl/stg64e231c1-4d37-4ad1-9b6e-e1d534e05cc2/GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:53,014] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:53,014] [INFO] Task started: HMMsearch
[2023-06-08 14:46:53,014] [INFO] Running command: hmmsearch --tblout GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/reference_markers.hmm GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:53,234] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:53,236] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64e231c1-4d37-4ad1-9b6e-e1d534e05cc2/GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 14:46:53,270] [INFO] Query marker FASTA was written to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:46:53,271] [INFO] Task started: Blastn
[2023-06-08 14:46:53,271] [INFO] Running command: blastn -query GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/reference_markers.fasta -out GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:53,813] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:53,817] [INFO] Selected 19 target genomes.
[2023-06-08 14:46:53,817] [INFO] Target genome list was writen to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:46:53,822] [INFO] Task started: fastANI
[2023-06-08 14:46:53,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg64e231c1-4d37-4ad1-9b6e-e1d534e05cc2/GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:47:02,384] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:02,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:47:02,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:47:02,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:47:02,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 14:47:02,386] [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 14:47:02,389] [INFO] DFAST Taxonomy check result was written to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:47:02,390] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:47:02,390] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:47:02,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/checkm_data
[2023-06-08 14:47:02,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:47:02,421] [INFO] Task started: CheckM
[2023-06-08 14:47:02,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:47:19,799] [INFO] Task succeeded: CheckM
[2023-06-08 14:47:19,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:47:19,822] [INFO] ===== Completeness check finished =====
[2023-06-08 14:47:19,823] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:47:19,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:47:19,824] [INFO] Task started: Blastn
[2023-06-08 14:47:19,824] [INFO] Running command: blastn -query GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d45dbe-d5fb-490b-a965-c3f3c6eccc88/dqc_reference/reference_markers_gtdb.fasta -out GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:20,568] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:20,573] [INFO] Selected 21 target genomes.
[2023-06-08 14:47:20,573] [INFO] Target genome list was writen to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:47:20,613] [INFO] Task started: fastANI
[2023-06-08 14:47:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg64e231c1-4d37-4ad1-9b6e-e1d534e05cc2/GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:26,046] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:26,064] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:47:26,064] [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_905215845.1	s__CAG-269 sp905215845	78.1097	81	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	78.043	122	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
GCA_001916005.1	s__CAG-269 sp001916005	77.8054	114	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_001915995.1	s__CAG-269 sp001915995	77.7243	121	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770415.1	s__CAG-452 sp900770415	77.6073	85	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	97.84	97.84	0.80	0.80	2	-
GCA_900551615.1	s__CAG-269 sp900551615	77.4988	110	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_900555085.1	s__Merdicola sp900555085	77.4756	94	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	99.34	98.84	0.87	0.87	3	-
GCA_904384245.1	s__CAG-269 sp904384245	77.4358	128	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904384205.1	s__CAG-269 sp904384205	77.4352	117	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770385.1	s__HGM13634 sp900770385	77.3962	105	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556695.1	s__CAG-269 sp900556695	77.388	88	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904381285.1	s__RGIG8482 sp904381285	77.3233	118	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410505.1	s__CAG-269 sp017410505	77.3162	107	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552655.1	s__Merdicola sp900552655	77.2975	95	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	98.23	98.11	0.86	0.84	4	-
GCA_900759015.1	s__Merdicola sp900759015	77.2752	85	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846485.1	s__CAG-269 sp014846485	77.1967	103	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001916065.1	s__CAG-269 sp001916065	77.1163	109	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.24	97.60	0.86	0.82	5	-
GCA_902760765.1	s__CAG-269 sp902760765	77.1041	59	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419495.1	s__CAG-269 sp904419495	77.0874	94	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754085.1	s__Merdicola sp900754085	76.9976	98	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	99.92	99.92	0.88	0.88	2	-
GCA_000434015.1	s__CAG-492 sp000434015	76.8272	118	563	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:26,066] [INFO] GTDB search result was written to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:26,067] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:26,070] [INFO] DFAST_QC result json was written to GCA_947088765.1_SRR14038232_bin.19_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:47:26,070] [INFO] DFAST_QC completed!
[2023-06-08 14:47:26,071] [INFO] Total running time: 0h0m38s