[2023-06-13 02:26:45,410] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:26:45,412] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:26:45,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference
[2023-06-13 02:26:47,490] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:26:47,492] [INFO] Task started: Prodigal
[2023-06-13 02:26:47,492] [INFO] Running command: gunzip -c /var/lib/cwl/stga75fa9c4-e1d3-4a62-b0d8-885fc4b78245/GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:26:52,771] [INFO] Task succeeded: Prodigal
[2023-06-13 02:26:52,772] [INFO] Task started: HMMsearch
[2023-06-13 02:26:52,772] [INFO] Running command: hmmsearch --tblout GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/reference_markers.hmm GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:26:53,010] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:26:53,011] [INFO] Found 6/6 markers.
[2023-06-13 02:26:53,038] [INFO] Query marker FASTA was written to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 02:26:53,038] [INFO] Task started: Blastn
[2023-06-13 02:26:53,038] [INFO] Running command: blastn -query GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/reference_markers.fasta -out GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:26:53,694] [INFO] Task succeeded: Blastn
[2023-06-13 02:26:53,699] [INFO] Selected 23 target genomes.
[2023-06-13 02:26:53,699] [INFO] Target genome list was writen to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:26:53,701] [INFO] Task started: fastANI
[2023-06-13 02:26:53,702] [INFO] Running command: fastANI --query /var/lib/cwl/stga75fa9c4-e1d3-4a62-b0d8-885fc4b78245/GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:27:02,974] [INFO] Task succeeded: fastANI
[2023-06-13 02:27:02,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:27:02,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:27:02,996] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:27:02,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:27:02,997] [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=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.5365	442	514	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.5311	441	514	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.4861	447	514	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0164	152	514	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7204	149	514	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6365	183	514	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.5581	187	514	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.2932	175	514	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.2358	115	514	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2143	160	514	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.0566	161	514	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.5469	150	514	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:27:02,999] [INFO] DFAST Taxonomy check result was written to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:27:03,000] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:27:03,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:27:03,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/checkm_data
[2023-06-13 02:27:03,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:27:03,029] [INFO] Task started: CheckM
[2023-06-13 02:27:03,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 02:27:24,718] [INFO] Task succeeded: CheckM
[2023-06-13 02:27:24,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:27:24,740] [INFO] ===== Completeness check finished =====
[2023-06-13 02:27:24,741] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:27:24,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:27:24,741] [INFO] Task started: Blastn
[2023-06-13 02:27:24,742] [INFO] Running command: blastn -query GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg79a3d41c-7a71-4ae4-b16a-d8af9d2130aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:27:25,813] [INFO] Task succeeded: Blastn
[2023-06-13 02:27:25,819] [INFO] Selected 40 target genomes.
[2023-06-13 02:27:25,819] [INFO] Target genome list was writen to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:27:25,833] [INFO] Task started: fastANI
[2023-06-13 02:27:25,833] [INFO] Running command: fastANI --query /var/lib/cwl/stga75fa9c4-e1d3-4a62-b0d8-885fc4b78245/GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:27:39,431] [INFO] Task succeeded: fastANI
[2023-06-13 02:27:39,458] [INFO] Found 36 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:27:39,459] [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_900754435.1	s__Collinsella sp900754435	99.2634	301	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0561	99.67	99.67	0.85	0.85	2	conclusive
GCF_001405375.1	s__Collinsella aerofaciens_F	94.8843	435	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	95.33	95.22	0.89	0.87	8	-
GCA_900542165.1	s__Collinsella sp900542165	94.531	421	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	95.41	95.20	0.86	0.82	3	-
GCA_900541135.1	s__Collinsella sp900541135	94.4144	421	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015553355.1	s__Collinsella aerofaciens_V	94.3948	425	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	96.92	0.91	0.91	2	-
GCA_900752015.1	s__Collinsella sp900752015	94.3815	414	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCA_900544645.1	s__Collinsella sp900544645	94.3357	388	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0848	N/A	N/A	N/A	N/A	1	-
GCF_015560765.1	s__Collinsella aerofaciens_M	94.3099	429	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	-
GCA_905209455.1	s__Collinsella sp905209455	94.2284	419	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1399	99.94	99.94	0.95	0.95	2	-
GCA_900544235.1	s__Collinsella sp900544235	94.2078	392	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.05	95.01	0.84	0.81	3	-
GCF_003438495.1	s__Collinsella sp003438495	94.1973	428	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900549065.1	s__Collinsella sp900549065	94.1926	375	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1036	N/A	N/A	N/A	N/A	1	-
GCA_905215765.1	s__Collinsella sp905215765	94.1651	369	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0331	95.09	95.09	0.79	0.79	2	-
GCA_900540995.1	s__Collinsella sp900540995	94.1512	418	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCF_015552075.1	s__Collinsella aerofaciens_Y	94.0539	421	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548815.1	s__Collinsella sp900548815	94.048	399	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543605.1	s__Collinsella sp900543605	94.0385	396	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215945.1	s__Collinsella sp905215945	94.0292	309	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2129	96.29	95.33	0.86	0.77	4	-
GCA_900545615.1	s__Collinsella sp900545615	94.0231	397	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900549355.1	s__Collinsella sp900549355	93.9252	352	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.83	0.83	2	-
GCA_905215835.1	s__Collinsella sp905215835	93.9178	364	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0274	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	93.9104	376	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552755.1	s__Collinsella sp900552755	93.8249	345	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549195.1	s__Collinsella sp900549195	93.8021	328	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762325.1	s__Collinsella sp900762325	93.7766	416	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541885.1	s__Collinsella sp900541885	93.776	427	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900547285.1	s__Collinsella sp900547285	93.7381	371	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545165.1	s__Collinsella sp900545165	93.7369	376	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549185.1	s__Collinsella sp900549185	93.6231	374	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760245.1	s__Collinsella sp900760245	93.5823	380	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551635.1	s__Collinsella sp900551635	93.5208	300	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.56	99.56	0.78	0.78	2	-
GCA_900553415.1	s__Collinsella sp900553415	93.2921	307	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546455.1	s__Collinsella sp900546455	93.2604	400	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549245.1	s__Collinsella sp900549245	93.2132	342	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556205.1	s__Collinsella sp900556205	93.1848	264	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551655.1	s__Collinsella sp900551655	92.9515	301	514	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 02:27:39,470] [INFO] GTDB search result was written to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:27:39,470] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:27:39,479] [INFO] DFAST_QC result json was written to GCA_938047175.1_ERR414448_bin.20_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:27:39,479] [INFO] DFAST_QC completed!
[2023-06-13 02:27:39,479] [INFO] Total running time: 0h0m54s