[2023-06-05 03:47:36,390] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:47:36,392] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:47:36,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference
[2023-06-05 03:47:38,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:47:38,370] [INFO] Task started: Prodigal
[2023-06-05 03:47:38,371] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcbda9ec-a387-4b7e-aa24-bae9d3cdbc13/GCA_934167635.1_ERR7738959_bin.257_genomic.fna.gz | prodigal -d GCA_934167635.1_ERR7738959_bin.257_genomic.fna/cds.fna -a GCA_934167635.1_ERR7738959_bin.257_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:47:40,797] [INFO] Task succeeded: Prodigal
[2023-06-05 03:47:40,797] [INFO] Task started: HMMsearch
[2023-06-05 03:47:40,798] [INFO] Running command: hmmsearch --tblout GCA_934167635.1_ERR7738959_bin.257_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/reference_markers.hmm GCA_934167635.1_ERR7738959_bin.257_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:47:41,028] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:47:41,029] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdcbda9ec-a387-4b7e-aa24-bae9d3cdbc13/GCA_934167635.1_ERR7738959_bin.257_genomic.fna.gz]
[2023-06-05 03:47:41,057] [INFO] Query marker FASTA was written to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/markers.fasta
[2023-06-05 03:47:41,058] [INFO] Task started: Blastn
[2023-06-05 03:47:41,058] [INFO] Running command: blastn -query GCA_934167635.1_ERR7738959_bin.257_genomic.fna/markers.fasta -db /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/reference_markers.fasta -out GCA_934167635.1_ERR7738959_bin.257_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:47:42,204] [INFO] Task succeeded: Blastn
[2023-06-05 03:47:42,208] [INFO] Selected 20 target genomes.
[2023-06-05 03:47:42,209] [INFO] Target genome list was writen to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/target_genomes.txt
[2023-06-05 03:47:42,210] [INFO] Task started: fastANI
[2023-06-05 03:47:42,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcbda9ec-a387-4b7e-aa24-bae9d3cdbc13/GCA_934167635.1_ERR7738959_bin.257_genomic.fna.gz --refList GCA_934167635.1_ERR7738959_bin.257_genomic.fna/target_genomes.txt --output GCA_934167635.1_ERR7738959_bin.257_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:47:50,744] [INFO] Task succeeded: fastANI
[2023-06-05 03:47:50,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:47:50,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:47:50,758] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:47:50,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:47:50,759] [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
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	75.2011	52	491	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	75.0932	50	491	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	75.0695	63	491	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	74.887	58	491	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	74.8122	59	491	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	74.7304	51	491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:47:50,761] [INFO] DFAST Taxonomy check result was written to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/tc_result.tsv
[2023-06-05 03:47:50,762] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:47:50,762] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:47:50,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/checkm_data
[2023-06-05 03:47:50,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:47:50,801] [INFO] Task started: CheckM
[2023-06-05 03:47:50,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934167635.1_ERR7738959_bin.257_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934167635.1_ERR7738959_bin.257_genomic.fna/checkm_input GCA_934167635.1_ERR7738959_bin.257_genomic.fna/checkm_result
[2023-06-05 03:48:06,222] [INFO] Task succeeded: CheckM
[2023-06-05 03:48:06,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:48:06,241] [INFO] ===== Completeness check finished =====
[2023-06-05 03:48:06,241] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:48:06,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934167635.1_ERR7738959_bin.257_genomic.fna/markers.fasta)
[2023-06-05 03:48:06,242] [INFO] Task started: Blastn
[2023-06-05 03:48:06,242] [INFO] Running command: blastn -query GCA_934167635.1_ERR7738959_bin.257_genomic.fna/markers.fasta -db /var/lib/cwl/stgda09ed50-8584-4e7e-9203-942af7eb7f1e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934167635.1_ERR7738959_bin.257_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:48:06,975] [INFO] Task succeeded: Blastn
[2023-06-05 03:48:06,980] [INFO] Selected 13 target genomes.
[2023-06-05 03:48:06,980] [INFO] Target genome list was writen to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:48:06,985] [INFO] Task started: fastANI
[2023-06-05 03:48:06,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcbda9ec-a387-4b7e-aa24-bae9d3cdbc13/GCA_934167635.1_ERR7738959_bin.257_genomic.fna.gz --refList GCA_934167635.1_ERR7738959_bin.257_genomic.fna/target_genomes_gtdb.txt --output GCA_934167635.1_ERR7738959_bin.257_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:48:10,993] [INFO] Task succeeded: fastANI
[2023-06-05 03:48:11,007] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:48:11,007] [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_000431335.1	s__CAG-269 sp000431335	98.0465	379	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	conclusive
GCA_900556945.1	s__CAG-269 sp900556945	82.3945	174	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.30	99.23	0.81	0.81	3	-
GCA_900554565.1	s__CAG-269 sp900554565	80.8466	259	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.93	97.94	0.90	0.85	3	-
GCA_900556695.1	s__CAG-269 sp900556695	80.8065	181	491	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_900762425.1	s__CAG-269 sp900762425	80.6695	250	491	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_905213875.1	s__CAG-269 sp905213875	80.4169	271	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	-
GCA_900554365.1	s__CAG-269 sp900554365	80.3234	223	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905215845.1	s__CAG-269 sp905215845	80.0432	147	491	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_014846485.1	s__CAG-269 sp014846485	79.7002	246	491	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	79.5227	217	491	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_001916005.1	s__CAG-269 sp001916005	79.3022	244	491	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_004553715.1	s__SFKP01 sp004553715	77.0511	103	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__SFKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404545.1	s__CAG-492 sp017404545	76.532	103	491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 03:48:11,014] [INFO] GTDB search result was written to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/result_gtdb.tsv
[2023-06-05 03:48:11,014] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:48:11,017] [INFO] DFAST_QC result json was written to GCA_934167635.1_ERR7738959_bin.257_genomic.fna/dqc_result.json
[2023-06-05 03:48:11,018] [INFO] DFAST_QC completed!
[2023-06-05 03:48:11,018] [INFO] Total running time: 0h0m35s