[2023-06-13 14:28:19,375] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:28:19,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:28:19,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference
[2023-06-13 14:28:21,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:28:21,025] [INFO] Task started: Prodigal
[2023-06-13 14:28:21,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg78865aec-a0a4-475b-947f-f94aecb97474/GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:28:27,097] [INFO] Task succeeded: Prodigal
[2023-06-13 14:28:27,098] [INFO] Task started: HMMsearch
[2023-06-13 14:28:27,098] [INFO] Running command: hmmsearch --tblout GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/reference_markers.hmm GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:28:27,325] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:28:27,327] [INFO] Found 6/6 markers.
[2023-06-13 14:28:27,350] [INFO] Query marker FASTA was written to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:28:27,351] [INFO] Task started: Blastn
[2023-06-13 14:28:27,351] [INFO] Running command: blastn -query GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/reference_markers.fasta -out GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:28:28,084] [INFO] Task succeeded: Blastn
[2023-06-13 14:28:28,090] [INFO] Selected 15 target genomes.
[2023-06-13 14:28:28,090] [INFO] Target genome list was writen to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:28:28,091] [INFO] Task started: fastANI
[2023-06-13 14:28:28,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg78865aec-a0a4-475b-947f-f94aecb97474/GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:28:34,408] [INFO] Task succeeded: fastANI
[2023-06-13 14:28:34,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:28:34,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:28:34,423] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:28:34,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:28:34,423] [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
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.3356	560	644	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.3318	555	644	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.2508	546	644	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.4796	229	644	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7928	213	644	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.7499	222	644	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.7003	260	644	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.6344	228	644	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6199	262	644	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.5508	227	644	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.2009	194	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:28:34,426] [INFO] DFAST Taxonomy check result was written to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:28:34,426] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:28:34,426] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:28:34,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/checkm_data
[2023-06-13 14:28:34,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:28:34,455] [INFO] Task started: CheckM
[2023-06-13 14:28:34,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:28:57,681] [INFO] Task succeeded: CheckM
[2023-06-13 14:28:57,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:28:57,705] [INFO] ===== Completeness check finished =====
[2023-06-13 14:28:57,705] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:28:57,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:28:57,706] [INFO] Task started: Blastn
[2023-06-13 14:28:57,706] [INFO] Running command: blastn -query GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgad5b5f8f-1194-493e-934f-a876ba69e21b/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:28:59,042] [INFO] Task succeeded: Blastn
[2023-06-13 14:28:59,047] [INFO] Selected 25 target genomes.
[2023-06-13 14:28:59,047] [INFO] Target genome list was writen to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:28:59,057] [INFO] Task started: fastANI
[2023-06-13 14:28:59,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg78865aec-a0a4-475b-947f-f94aecb97474/GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:29:09,902] [INFO] Task succeeded: fastANI
[2023-06-13 14:29:09,933] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:29:09,934] [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_900541475.1	s__Collinsella sp900541475	100.0	623	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.73	95.01	0.89	0.85	4	conclusive
GCA_905215815.1	s__Collinsella sp905215815	94.7159	482	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.63	95.53	0.85	0.84	3	-
GCA_900549455.1	s__Collinsella sp900549455	94.6479	452	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.06	95.06	0.86	0.86	2	-
GCA_900752275.1	s__Collinsella sp900752275	94.6256	414	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761145.1	s__Collinsella sp900761145	94.206	500	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545075.1	s__Collinsella sp900545075	93.8904	472	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.97	98.97	0.86	0.86	2	-
GCA_900758375.1	s__Collinsella sp900758375	93.763	486	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.06	0.83	0.78	8	-
GCA_900540945.1	s__Collinsella sp900540945	93.5044	527	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.33	0.85	0.84	5	-
GCA_008680965.1	s__Collinsella aerofaciens_L	93.4543	552	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.14	95.14	0.89	0.89	2	-
GCA_905215205.1	s__Collinsella sp905215205	93.2428	376	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756725.1	s__Collinsella sp900756725	93.2315	451	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
GCA_900541045.1	s__Collinsella sp900541045	93.2227	506	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555955.1	s__Collinsella sp900555955	92.654	280	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.54	99.54	0.80	0.80	2	-
GCA_900549745.1	s__Collinsella sp900549745	92.5052	473	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1078	95.40	95.40	0.87	0.87	2	-
GCA_900541065.1	s__Collinsella sp900541065	92.3225	548	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0334	N/A	N/A	N/A	N/A	1	-
GCA_900543845.1	s__Collinsella sp900543845	92.2959	496	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.22	0.88	0.81	3	-
GCA_905215835.1	s__Collinsella sp905215835	92.2355	440	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0274	N/A	N/A	N/A	N/A	1	-
GCA_902388345.1	s__Collinsella sp902388345	92.1914	502	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.97	0.98	0.97	3	-
GCA_905215765.1	s__Collinsella sp905215765	92.1893	444	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0331	95.09	95.09	0.79	0.79	2	-
GCA_905215755.1	s__Collinsella sp905215755	92.1541	513	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0833	N/A	N/A	N/A	N/A	1	-
GCA_905215095.1	s__Collinsella sp905215095	92.0548	345	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.84	0.84	2	-
GCA_900549245.1	s__Collinsella sp900549245	92.0034	415	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542325.1	s__Collinsella sp900542325	91.9263	520	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900550835.1	s__Collinsella sp900550835	91.6885	416	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.40	95.47	0.90	0.85	4	-
GCF_015557435.1	s__Collinsella aerofaciens_Z	91.3989	522	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:29:09,936] [INFO] GTDB search result was written to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:29:09,936] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:29:09,940] [INFO] DFAST_QC result json was written to GCA_938041095.1_ERR1018268_bin.101_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:29:09,941] [INFO] DFAST_QC completed!
[2023-06-13 14:29:09,941] [INFO] Total running time: 0h0m51s