[2023-06-16 20:59:43,869] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:59:43,870] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:59:43,871] [INFO] DQC Reference Directory: /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference
[2023-06-16 20:59:44,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:59:44,974] [INFO] Task started: Prodigal
[2023-06-16 20:59:44,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg74a256f1-39db-4060-93c0-e0379727408f/GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna.gz | prodigal -d GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/cds.fna -a GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:59:50,582] [INFO] Task succeeded: Prodigal
[2023-06-16 20:59:50,583] [INFO] Task started: HMMsearch
[2023-06-16 20:59:50,583] [INFO] Running command: hmmsearch --tblout GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/reference_markers.hmm GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:59:50,763] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:59:50,764] [INFO] Found 6/6 markers.
[2023-06-16 20:59:50,785] [INFO] Query marker FASTA was written to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/markers.fasta
[2023-06-16 20:59:50,785] [INFO] Task started: Blastn
[2023-06-16 20:59:50,785] [INFO] Running command: blastn -query GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/reference_markers.fasta -out GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:59:51,362] [INFO] Task succeeded: Blastn
[2023-06-16 20:59:51,365] [INFO] Selected 14 target genomes.
[2023-06-16 20:59:51,366] [INFO] Target genome list was writen to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/target_genomes.txt
[2023-06-16 20:59:51,366] [INFO] Task started: fastANI
[2023-06-16 20:59:51,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a256f1-39db-4060-93c0-e0379727408f/GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna.gz --refList GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/target_genomes.txt --output GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:59:58,844] [INFO] Task succeeded: fastANI
[2023-06-16 20:59:58,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:59:58,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:59:58,854] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:59:58,854] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:59:58,854] [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 phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	80.8848	329	717	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.5787	223	717	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.5775	240	717	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.5124	211	717	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9599	182	717	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.872	177	717	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.8134	176	717	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.7065	130	717	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.3642	142	717	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.1723	80	717	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.1506	115	717	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.0236	90	717	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.7638	91	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:59:58,856] [INFO] DFAST Taxonomy check result was written to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/tc_result.tsv
[2023-06-16 20:59:58,856] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:59:58,856] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:59:58,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/checkm_data
[2023-06-16 20:59:58,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:59:58,883] [INFO] Task started: CheckM
[2023-06-16 20:59:58,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/checkm_input GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/checkm_result
[2023-06-16 21:00:19,338] [INFO] Task succeeded: CheckM
[2023-06-16 21:00:19,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.46%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:00:19,355] [INFO] ===== Completeness check finished =====
[2023-06-16 21:00:19,356] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:00:19,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/markers.fasta)
[2023-06-16 21:00:19,356] [INFO] Task started: Blastn
[2023-06-16 21:00:19,356] [INFO] Running command: blastn -query GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stgec34a2a8-4f88-42d3-9988-beecfe17f863/dqc_reference/reference_markers_gtdb.fasta -out GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:00:20,369] [INFO] Task succeeded: Blastn
[2023-06-16 21:00:20,372] [INFO] Selected 18 target genomes.
[2023-06-16 21:00:20,372] [INFO] Target genome list was writen to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:00:20,382] [INFO] Task started: fastANI
[2023-06-16 21:00:20,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a256f1-39db-4060-93c0-e0379727408f/GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna.gz --refList GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/target_genomes_gtdb.txt --output GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:00:29,961] [INFO] Task succeeded: fastANI
[2023-06-16 21:00:29,970] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:00:29,970] [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_900549405.1	s__Lawsonibacter sp900549405	97.9582	546	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	conclusive
GCF_014287875.1	s__Lawsonibacter sp014287875	93.0574	542	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCA_900550705.1	s__Lawsonibacter sp900550705	84.1796	326	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003478995.1	s__Lawsonibacter sp003478995	81.744	365	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_904420465.1	s__Lawsonibacter sp904420465	81.5181	324	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899775.1	s__Lawsonibacter sp900545895	81.4967	365	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.62	96.12	0.85	0.79	4	-
GCA_000492175.1	s__Lawsonibacter sp000492175	81.3039	337	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585815.1	s__Lawsonibacter sp910585815	81.218	348	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584605.1	s__Lawsonibacter sp910584605	80.926	303	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161175.1	s__Lawsonibacter sp002161175	80.9189	308	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612335.1	s__Lawsonibacter sp003612335	80.6243	339	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215425.1	s__Lawsonibacter sp905215425	79.7454	142	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	78.3599	200	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_904419145.1	s__CAJFPI01 sp904419145	77.8649	147	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	98.67	98.54	0.90	0.87	4	-
GCF_004154955.1	s__Intestinimonas butyriciproducens	77.8445	178	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.73	98.09	0.87	0.79	17	-
--------------------------------------------------------------------------------
[2023-06-16 21:00:29,972] [INFO] GTDB search result was written to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/result_gtdb.tsv
[2023-06-16 21:00:29,973] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:00:29,976] [INFO] DFAST_QC result json was written to GCA_905206655.1_ERR1600597-mag-bin.16_genomic.fna/dqc_result.json
[2023-06-16 21:00:29,976] [INFO] DFAST_QC completed!
[2023-06-16 21:00:29,976] [INFO] Total running time: 0h0m46s