[2023-06-13 05:03:15,398] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:03:15,400] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:03:15,400] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference
[2023-06-13 05:03:17,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:03:17,191] [INFO] Task started: Prodigal
[2023-06-13 05:03:17,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg870bc8fa-94d4-4706-b694-5f781c547243/GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:03:22,493] [INFO] Task succeeded: Prodigal
[2023-06-13 05:03:22,493] [INFO] Task started: HMMsearch
[2023-06-13 05:03:22,493] [INFO] Running command: hmmsearch --tblout GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/reference_markers.hmm GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:03:22,719] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:03:22,720] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg870bc8fa-94d4-4706-b694-5f781c547243/GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 05:03:22,742] [INFO] Query marker FASTA was written to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 05:03:22,742] [INFO] Task started: Blastn
[2023-06-13 05:03:22,742] [INFO] Running command: blastn -query GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/reference_markers.fasta -out GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:03:23,428] [INFO] Task succeeded: Blastn
[2023-06-13 05:03:23,447] [INFO] Selected 19 target genomes.
[2023-06-13 05:03:23,448] [INFO] Target genome list was writen to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:03:23,453] [INFO] Task started: fastANI
[2023-06-13 05:03:23,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg870bc8fa-94d4-4706-b694-5f781c547243/GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:03:32,067] [INFO] Task succeeded: fastANI
[2023-06-13 05:03:32,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:03:32,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:03:32,081] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:03:32,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:03:32,081] [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	94.3846	456	522	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.3768	465	522	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.2842	460	522	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	79.6223	183	522	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.2147	192	522	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.1233	169	522	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.1114	192	522	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.1019	171	522	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.6003	159	522	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:03:32,084] [INFO] DFAST Taxonomy check result was written to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:03:32,085] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:03:32,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:03:32,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/checkm_data
[2023-06-13 05:03:32,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:03:32,113] [INFO] Task started: CheckM
[2023-06-13 05:03:32,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 05:03:54,150] [INFO] Task succeeded: CheckM
[2023-06-13 05:03:54,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.44%
Contamintation: 7.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:03:54,182] [INFO] ===== Completeness check finished =====
[2023-06-13 05:03:54,183] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:03:54,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:03:54,184] [INFO] Task started: Blastn
[2023-06-13 05:03:54,184] [INFO] Running command: blastn -query GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe3b01a7-1a95-4e25-b180-6784bddaf94a/dqc_reference/reference_markers_gtdb.fasta -out GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:03:55,427] [INFO] Task succeeded: Blastn
[2023-06-13 05:03:55,433] [INFO] Selected 34 target genomes.
[2023-06-13 05:03:55,433] [INFO] Target genome list was writen to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:03:55,445] [INFO] Task started: fastANI
[2023-06-13 05:03:55,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg870bc8fa-94d4-4706-b694-5f781c547243/GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:04:09,058] [INFO] Task succeeded: fastANI
[2023-06-13 05:04:09,099] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 05:04:09,099] [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_900541125.1	s__Collinsella sp900541125	94.4837	445	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2242	95.44	95.26	0.87	0.84	10	-
GCA_018380015.1	s__Collinsella sp018380015	94.3581	447	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCA_018381235.1	s__Collinsella sp018381235	94.2972	439	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0673	N/A	N/A	N/A	N/A	1	-
GCF_000763055.1	s__Collinsella sp000763055	94.267	458	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005844325.1	s__Collinsella aerofaciens_G	94.2551	441	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.009	96.00	95.07	0.90	0.86	20	-
GCF_015553355.1	s__Collinsella aerofaciens_V	94.2411	448	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	96.92	0.91	0.91	2	-
GCA_014871665.1	s__Collinsella sp014871665	94.2302	422	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1702	95.19	95.19	0.85	0.85	2	-
GCA_900544235.1	s__Collinsella sp900544235	94.2075	424	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.05	95.01	0.84	0.81	3	-
GCA_900547345.1	s__Collinsella sp900547345	94.2055	398	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0188	95.15	95.15	0.87	0.87	2	-
GCA_900548495.1	s__Collinsella sp900548495	94.1982	399	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0367	N/A	N/A	N/A	N/A	1	-
GCA_900752215.1	s__Collinsella sp900752215	94.1966	404	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0875	99.95	99.95	0.94	0.94	2	-
GCA_900542555.1	s__Collinsella sp900542555	94.174	418	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215835.1	s__Collinsella sp905215835	94.1034	377	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0274	N/A	N/A	N/A	N/A	1	-
GCA_900542305.1	s__Collinsella sp900542305	93.9587	433	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905213725.1	s__Collinsella aerofaciens_R	93.9496	381	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0706	99.79	99.79	0.97	0.97	2	-
GCA_900540935.1	s__Collinsella sp900540935	93.9466	438	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.34	95.21	0.87	0.87	3	-
GCA_900540895.1	s__Collinsella sp900540895	93.9034	445	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_905208345.1	s__Collinsella sp905208345	93.8482	389	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900544205.1	s__Collinsella sp900544205	93.7928	403	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900762325.1	s__Collinsella sp900762325	93.6067	434	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751665.1	s__Collinsella sp900751665	93.5467	346	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.75	99.75	0.87	0.87	2	-
GCA_905204635.1	s__Collinsella sp905204635	93.513	322	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018368345.1	s__Collinsella sp018368345	93.437	441	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198825.1	s__Collinsella sp905198825	93.2278	305	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555355.1	s__Collinsella sp900555355	92.9392	319	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.56	97.56	0.72	0.72	2	-
GCA_900545445.1	s__Collinsella sp900545445	92.7507	413	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.18	95.16	0.86	0.84	3	-
GCA_900542085.1	s__Collinsella sp900542085	92.2705	416	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900767675.1	s__Collinsella sp900767675	92.0525	429	522	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846205.1	s__Collinsella aerofaciens_AE	90.1498	222	522	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 05:04:09,102] [INFO] GTDB search result was written to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:04:09,102] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:04:09,107] [INFO] DFAST_QC result json was written to GCA_938030545.1_ERR912138_bin.42_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:04:09,108] [INFO] DFAST_QC completed!
[2023-06-13 05:04:09,108] [INFO] Total running time: 0h0m54s