[2023-06-19 01:08:34,400] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:08:34,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:08:34,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference
[2023-06-19 01:08:35,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:08:35,710] [INFO] Task started: Prodigal
[2023-06-19 01:08:35,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f15b158-7c63-4c0f-80f9-30f395297bb1/GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:08:39,882] [INFO] Task succeeded: Prodigal
[2023-06-19 01:08:39,882] [INFO] Task started: HMMsearch
[2023-06-19 01:08:39,882] [INFO] Running command: hmmsearch --tblout GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/reference_markers.hmm GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:08:40,114] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:08:40,117] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6f15b158-7c63-4c0f-80f9-30f395297bb1/GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-19 01:08:40,141] [INFO] Query marker FASTA was written to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 01:08:40,142] [INFO] Task started: Blastn
[2023-06-19 01:08:40,142] [INFO] Running command: blastn -query GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/reference_markers.fasta -out GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:08:40,736] [INFO] Task succeeded: Blastn
[2023-06-19 01:08:40,743] [INFO] Selected 19 target genomes.
[2023-06-19 01:08:40,743] [INFO] Target genome list was writen to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 01:08:40,752] [INFO] Task started: fastANI
[2023-06-19 01:08:40,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f15b158-7c63-4c0f-80f9-30f395297bb1/GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:08:53,539] [INFO] Task succeeded: fastANI
[2023-06-19 01:08:53,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:08:53,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:08:53,547] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 01:08:53,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 01:08:53,548] [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
Amedibacillus dolichus	strain=DSM 3991	GCA_000154285.1	31971	31971	type	True	98.9307	562	594	95	conclusive
[Clostridium] innocuum	strain=ATCC 14501	GCA_012317185.1	1522	1522	type	True	77.7554	98	594	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_018458805.1	1522	1522	type	True	77.6859	95	594	95	below_threshold
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	77.6189	102	594	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_004341945.1	1796635	1796635	type	True	77.499	101	594	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	77.3883	101	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:08:53,553] [INFO] DFAST Taxonomy check result was written to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 01:08:53,554] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:08:53,554] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:08:53,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/checkm_data
[2023-06-19 01:08:53,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:08:53,579] [INFO] Task started: CheckM
[2023-06-19 01:08:53,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 01:09:13,747] [INFO] Task succeeded: CheckM
[2023-06-19 01:09:13,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:09:13,770] [INFO] ===== Completeness check finished =====
[2023-06-19 01:09:13,770] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:09:13,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 01:09:13,771] [INFO] Task started: Blastn
[2023-06-19 01:09:13,771] [INFO] Running command: blastn -query GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95152d9-0ca8-464f-a0bb-797bb48adaab/dqc_reference/reference_markers_gtdb.fasta -out GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:09:14,705] [INFO] Task succeeded: Blastn
[2023-06-19 01:09:14,715] [INFO] Selected 20 target genomes.
[2023-06-19 01:09:14,715] [INFO] Target genome list was writen to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:09:14,738] [INFO] Task started: fastANI
[2023-06-19 01:09:14,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f15b158-7c63-4c0f-80f9-30f395297bb1/GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:09:26,085] [INFO] Task succeeded: fastANI
[2023-06-19 01:09:26,095] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:09:26,095] [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
GCF_000154285.1	s__Amedibacillus dolichus	98.9307	562	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacillus	95.0	99.06	98.73	0.91	0.85	7	conclusive
GCF_014337235.1	s__NSJ-61 sp003433845	78.0658	91	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
GCF_012317185.1	s__Clostridium_AQ innocuum	77.7554	98	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.93	97.20	0.87	0.81	50	-
GCA_900552125.1	s__Clostridium_AQ sp900552125	77.6796	107	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.93	99.93	0.86	0.86	2	-
GCA_910576345.1	s__C-19 sp910576345	77.6715	54	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	99.11	99.11	0.92	0.92	2	-
GCF_010537335.1	s__Amedibacterium intestinale	77.6189	102	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCF_004341945.1	s__Longicatena caecimuris	77.499	101	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	-
GCA_017161075.1	s__Clostridium_AQ sp000165065	77.3185	101	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCA_003481775.1	s__Clostridium_AQ sp003481775	77.2162	100	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.27	97.98	0.91	0.82	5	-
GCA_009917405.1	s__C-19 sp009917405	76.6986	52	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576855.1	s__C-19 sp910576855	76.6165	59	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	99.07	99.07	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-19 01:09:26,097] [INFO] GTDB search result was written to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 01:09:26,098] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:09:26,102] [INFO] DFAST_QC result json was written to GCA_937997905.1_SRR12395700_bin.36_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 01:09:26,102] [INFO] DFAST_QC completed!
[2023-06-19 01:09:26,102] [INFO] Total running time: 0h0m52s