[2023-06-28 04:20:28,897] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:28,901] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:28,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference
[2023-06-28 04:20:30,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:30,191] [INFO] Task started: Prodigal
[2023-06-28 04:20:30,191] [INFO] Running command: gunzip -c /var/lib/cwl/stgef148cbc-86ce-4f49-bd1d-9e0bc06398b9/GCA_944388045.1_BRZ_HA_bin44_genomic.fna.gz | prodigal -d GCA_944388045.1_BRZ_HA_bin44_genomic.fna/cds.fna -a GCA_944388045.1_BRZ_HA_bin44_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:33,033] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:33,034] [INFO] Task started: HMMsearch
[2023-06-28 04:20:33,034] [INFO] Running command: hmmsearch --tblout GCA_944388045.1_BRZ_HA_bin44_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/reference_markers.hmm GCA_944388045.1_BRZ_HA_bin44_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:33,335] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:33,337] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgef148cbc-86ce-4f49-bd1d-9e0bc06398b9/GCA_944388045.1_BRZ_HA_bin44_genomic.fna.gz]
[2023-06-28 04:20:33,364] [INFO] Query marker FASTA was written to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/markers.fasta
[2023-06-28 04:20:33,364] [INFO] Task started: Blastn
[2023-06-28 04:20:33,364] [INFO] Running command: blastn -query GCA_944388045.1_BRZ_HA_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/reference_markers.fasta -out GCA_944388045.1_BRZ_HA_bin44_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:33,974] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:33,977] [INFO] Selected 25 target genomes.
[2023-06-28 04:20:33,978] [INFO] Target genome list was writen to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/target_genomes.txt
[2023-06-28 04:20:33,984] [INFO] Task started: fastANI
[2023-06-28 04:20:33,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgef148cbc-86ce-4f49-bd1d-9e0bc06398b9/GCA_944388045.1_BRZ_HA_bin44_genomic.fna.gz --refList GCA_944388045.1_BRZ_HA_bin44_genomic.fna/target_genomes.txt --output GCA_944388045.1_BRZ_HA_bin44_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:45,571] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:45,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:45,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:45,585] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:45,586] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:20:45,586] [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 bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	75.1659	55	576	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	74.9592	65	576	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	74.9376	68	576	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	74.9143	58	576	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	74.9051	62	576	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	74.8898	69	576	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	74.8847	58	576	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	74.8228	68	576	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	74.8082	64	576	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	74.7971	67	576	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	74.7971	67	576	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	74.7662	94	576	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	74.7462	93	576	95	below_threshold
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	74.7396	84	576	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	74.7312	98	576	95	below_threshold
Marinitoga litoralis	strain=DSM 21709	GCA_016908145.1	570855	570855	type	True	74.7294	57	576	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:20:45,588] [INFO] DFAST Taxonomy check result was written to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/tc_result.tsv
[2023-06-28 04:20:45,588] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:45,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:45,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/checkm_data
[2023-06-28 04:20:45,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:45,615] [INFO] Task started: CheckM
[2023-06-28 04:20:45,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944388045.1_BRZ_HA_bin44_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944388045.1_BRZ_HA_bin44_genomic.fna/checkm_input GCA_944388045.1_BRZ_HA_bin44_genomic.fna/checkm_result
[2023-06-28 04:21:02,769] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:02,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:21:02,792] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:02,792] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:02,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944388045.1_BRZ_HA_bin44_genomic.fna/markers.fasta)
[2023-06-28 04:21:02,793] [INFO] Task started: Blastn
[2023-06-28 04:21:02,793] [INFO] Running command: blastn -query GCA_944388045.1_BRZ_HA_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stg8262c678-7d89-44b3-8037-6b0d77ace213/dqc_reference/reference_markers_gtdb.fasta -out GCA_944388045.1_BRZ_HA_bin44_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:03,588] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:03,592] [INFO] Selected 14 target genomes.
[2023-06-28 04:21:03,592] [INFO] Target genome list was writen to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:03,595] [INFO] Task started: fastANI
[2023-06-28 04:21:03,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgef148cbc-86ce-4f49-bd1d-9e0bc06398b9/GCA_944388045.1_BRZ_HA_bin44_genomic.fna.gz --refList GCA_944388045.1_BRZ_HA_bin44_genomic.fna/target_genomes_gtdb.txt --output GCA_944388045.1_BRZ_HA_bin44_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:08,042] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:08,063] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:21:08,063] [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_001915995.1	s__CAG-269 sp001915995	82.1638	283	576	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	81.894	303	576	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_017409455.1	s__CAG-269 sp017409455	79.9947	207	576	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_001916055.1	s__CAG-269 sp001916055	79.9335	227	576	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.37	97.96	0.88	0.86	4	-
GCA_900555615.1	s__CAG-269 sp900555615	79.7738	227	576	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	97.95	97.78	0.76	0.74	3	-
GCA_905215845.1	s__CAG-269 sp905215845	78.6233	119	576	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_900554565.1	s__CAG-269 sp900554565	78.4363	165	576	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	78.3998	141	576	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	78.2387	205	576	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_017404025.1	s__CAG-269 sp017404025	78.1421	168	576	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	78.0337	199	576	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_904387305.1	s__CAG-269 sp904387305	78.0157	183	576	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_017533795.1	s__CAG-269 sp017533795	77.2052	138	576	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_017528375.1	s__CAG-492 sp017528375	76.8374	119	576	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	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:08,065] [INFO] GTDB search result was written to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:08,066] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:08,071] [INFO] DFAST_QC result json was written to GCA_944388045.1_BRZ_HA_bin44_genomic.fna/dqc_result.json
[2023-06-28 04:21:08,071] [INFO] DFAST_QC completed!
[2023-06-28 04:21:08,071] [INFO] Total running time: 0h0m39s