[2023-06-28 11:29:29,664] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:29:29,666] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:29:29,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference
[2023-06-28 11:29:30,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:29:30,760] [INFO] Task started: Prodigal
[2023-06-28 11:29:30,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg1194adbc-56ad-449d-ad8d-d2643c27ec99/GCA_944321335.1_BRZ_SF_bin128_genomic.fna.gz | prodigal -d GCA_944321335.1_BRZ_SF_bin128_genomic.fna/cds.fna -a GCA_944321335.1_BRZ_SF_bin128_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:29:41,946] [INFO] Task succeeded: Prodigal
[2023-06-28 11:29:41,946] [INFO] Task started: HMMsearch
[2023-06-28 11:29:41,946] [INFO] Running command: hmmsearch --tblout GCA_944321335.1_BRZ_SF_bin128_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/reference_markers.hmm GCA_944321335.1_BRZ_SF_bin128_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:29:42,127] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:29:42,128] [INFO] Found 6/6 markers.
[2023-06-28 11:29:42,149] [INFO] Query marker FASTA was written to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/markers.fasta
[2023-06-28 11:29:42,149] [INFO] Task started: Blastn
[2023-06-28 11:29:42,150] [INFO] Running command: blastn -query GCA_944321335.1_BRZ_SF_bin128_genomic.fna/markers.fasta -db /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/reference_markers.fasta -out GCA_944321335.1_BRZ_SF_bin128_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:29:42,716] [INFO] Task succeeded: Blastn
[2023-06-28 11:29:42,719] [INFO] Selected 20 target genomes.
[2023-06-28 11:29:42,719] [INFO] Target genome list was writen to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/target_genomes.txt
[2023-06-28 11:29:42,758] [INFO] Task started: fastANI
[2023-06-28 11:29:42,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg1194adbc-56ad-449d-ad8d-d2643c27ec99/GCA_944321335.1_BRZ_SF_bin128_genomic.fna.gz --refList GCA_944321335.1_BRZ_SF_bin128_genomic.fna/target_genomes.txt --output GCA_944321335.1_BRZ_SF_bin128_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:29:56,225] [INFO] Task succeeded: fastANI
[2023-06-28 11:29:56,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:29:56,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:29:56,237] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:29:56,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:29:56,237] [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
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.0277	256	841	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	78.975	299	841	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	78.9499	299	841	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.8829	262	841	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.84	252	841	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.6593	250	841	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.5182	246	841	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	77.7226	170	841	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	77.7042	147	841	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	77.7034	150	841	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.6778	162	841	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.6344	211	841	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	77.602	154	841	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	77.5065	101	841	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	77.4534	102	841	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	77.4431	104	841	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.3213	108	841	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	77.2593	93	841	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.2578	133	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:29:56,239] [INFO] DFAST Taxonomy check result was written to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/tc_result.tsv
[2023-06-28 11:29:56,239] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:29:56,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:29:56,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/checkm_data
[2023-06-28 11:29:56,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:29:56,268] [INFO] Task started: CheckM
[2023-06-28 11:29:56,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321335.1_BRZ_SF_bin128_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321335.1_BRZ_SF_bin128_genomic.fna/checkm_input GCA_944321335.1_BRZ_SF_bin128_genomic.fna/checkm_result
[2023-06-28 11:30:30,887] [INFO] Task succeeded: CheckM
[2023-06-28 11:30:30,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:30:30,904] [INFO] ===== Completeness check finished =====
[2023-06-28 11:30:30,904] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:30:30,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321335.1_BRZ_SF_bin128_genomic.fna/markers.fasta)
[2023-06-28 11:30:30,905] [INFO] Task started: Blastn
[2023-06-28 11:30:30,905] [INFO] Running command: blastn -query GCA_944321335.1_BRZ_SF_bin128_genomic.fna/markers.fasta -db /var/lib/cwl/stg147ae008-cb26-492f-ab38-9c43c40ab625/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321335.1_BRZ_SF_bin128_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:30:31,737] [INFO] Task succeeded: Blastn
[2023-06-28 11:30:31,740] [INFO] Selected 20 target genomes.
[2023-06-28 11:30:31,740] [INFO] Target genome list was writen to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:30:31,776] [INFO] Task started: fastANI
[2023-06-28 11:30:31,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg1194adbc-56ad-449d-ad8d-d2643c27ec99/GCA_944321335.1_BRZ_SF_bin128_genomic.fna.gz --refList GCA_944321335.1_BRZ_SF_bin128_genomic.fna/target_genomes_gtdb.txt --output GCA_944321335.1_BRZ_SF_bin128_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:30:43,812] [INFO] Task succeeded: fastANI
[2023-06-28 11:30:43,824] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 11:30:43,825] [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_900128495.1	s__Phocaeicola ilei	79.596	380	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_900553185.1	s__Phocaeicola sp900553185	79.223	183	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.0345	208	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.034	187	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013618865.1	s__Phocaeicola sp900541515	79.0097	257	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_000374585.1	s__Phocaeicola barnesiae	78.9532	301	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_000432735.1	s__Phocaeicola sp000432735	78.9252	279	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCF_000154845.1	s__Phocaeicola coprocola	78.8829	262	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	78.8505	249	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_000187895.1	s__Phocaeicola plebeius	78.8429	251	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_003437535.1	s__Phocaeicola plebeius_A	78.8173	260	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_016900355.1	s__Phocaeicola sp900551065	78.7559	253	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_000157915.1	s__Phocaeicola coprophilus	78.6529	251	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	78.6436	264	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCA_900556845.1	s__Phocaeicola sp900556845	78.4428	101	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.4235	215	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_900551645.1	s__Phocaeicola sp900551645	78.218	198	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_900546645.1	s__Phocaeicola sp900546645	77.9778	165	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.94	98.88	0.79	0.75	3	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.4679	126	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388495.1	s__Bacteroides sp902388495	77.2423	109	841	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-28 11:30:43,826] [INFO] GTDB search result was written to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/result_gtdb.tsv
[2023-06-28 11:30:43,827] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:30:43,830] [INFO] DFAST_QC result json was written to GCA_944321335.1_BRZ_SF_bin128_genomic.fna/dqc_result.json
[2023-06-28 11:30:43,830] [INFO] DFAST_QC completed!
[2023-06-28 11:30:43,830] [INFO] Total running time: 0h1m14s