[2023-06-14 01:14:04,398] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:14:04,400] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:14:04,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference
[2023-06-14 01:14:06,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:14:06,897] [INFO] Task started: Prodigal
[2023-06-14 01:14:06,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9796176-26d5-4e6c-aee3-cc217790a7f2/GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:14:16,685] [INFO] Task succeeded: Prodigal
[2023-06-14 01:14:16,686] [INFO] Task started: HMMsearch
[2023-06-14 01:14:16,686] [INFO] Running command: hmmsearch --tblout GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/reference_markers.hmm GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:14:16,909] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:14:16,910] [INFO] Found 6/6 markers.
[2023-06-14 01:14:16,932] [INFO] Query marker FASTA was written to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:14:16,932] [INFO] Task started: Blastn
[2023-06-14 01:14:16,932] [INFO] Running command: blastn -query GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/reference_markers.fasta -out GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:14:17,539] [INFO] Task succeeded: Blastn
[2023-06-14 01:14:17,543] [INFO] Selected 13 target genomes.
[2023-06-14 01:14:17,543] [INFO] Target genome list was writen to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:14:17,576] [INFO] Task started: fastANI
[2023-06-14 01:14:17,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9796176-26d5-4e6c-aee3-cc217790a7f2/GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:14:25,109] [INFO] Task succeeded: fastANI
[2023-06-14 01:14:25,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:14:25,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:14:25,124] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:14:25,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:14:25,124] [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
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	80.7419	364	538	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	80.7203	359	538	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	80.7154	334	538	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	80.7032	368	538	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.4918	361	538	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	80.491	349	538	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.4557	358	538	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	80.0769	336	538	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	80.0026	327	538	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	79.9996	314	538	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	79.919	327	538	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	78.735	259	538	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.3237	94	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:14:25,127] [INFO] DFAST Taxonomy check result was written to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:14:25,127] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:14:25,128] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:14:25,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/checkm_data
[2023-06-14 01:14:25,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:14:25,153] [INFO] Task started: CheckM
[2023-06-14 01:14:25,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:14:55,727] [INFO] Task succeeded: CheckM
[2023-06-14 01:14:55,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:14:55,749] [INFO] ===== Completeness check finished =====
[2023-06-14 01:14:55,750] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:14:55,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:14:55,751] [INFO] Task started: Blastn
[2023-06-14 01:14:55,751] [INFO] Running command: blastn -query GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg756204ea-c050-4341-bbb0-805270baf0df/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:14:56,653] [INFO] Task succeeded: Blastn
[2023-06-14 01:14:56,658] [INFO] Selected 12 target genomes.
[2023-06-14 01:14:56,658] [INFO] Target genome list was writen to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:14:56,667] [INFO] Task started: fastANI
[2023-06-14 01:14:56,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9796176-26d5-4e6c-aee3-cc217790a7f2/GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:15:02,847] [INFO] Task succeeded: fastANI
[2023-06-14 01:15:02,863] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:15:02,863] [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_002428825.1	s__Alistipes sp002428825	98.5627	493	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.47	98.29	0.93	0.91	4	conclusive
GCA_014796635.1	s__Alistipes sp014796635	84.7562	266	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575495.1	s__Alistipes sp910575495	84.3658	423	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.23	98.47	0.95	0.90	3	-
GCA_910580175.1	s__Alistipes sp910580175	82.8916	412	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553175.1	s__Alistipes sp900553175	81.9711	259	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542685.1	s__Alistipes dispar	80.7336	333	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCF_000312145.1	s__Alistipes senegalensis	80.7041	369	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_900542505.1	s__Alistipes stercorigallinarum	80.6378	290	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCF_000265365.1	s__Alistipes finegoldii	80.0739	335	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_019115745.1	s__Alistipes intestinigallinarum	79.8265	277	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119615.1	s__Alistipes stercoravium	79.6907	281	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCF_006542665.1	s__Alistipes communis	78.7516	258	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	-
--------------------------------------------------------------------------------
[2023-06-14 01:15:02,865] [INFO] GTDB search result was written to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:15:02,866] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:15:02,870] [INFO] DFAST_QC result json was written to GCA_947178855.1_SRR13713023_bin.7_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:15:02,870] [INFO] DFAST_QC completed!
[2023-06-14 01:15:02,870] [INFO] Total running time: 0h0m58s