[2023-06-13 17:11:53,817] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:11:53,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:11:53,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference
[2023-06-13 17:11:55,262] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:11:55,263] [INFO] Task started: Prodigal
[2023-06-13 17:11:55,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bb3480f-996c-4838-ab23-0f0d073ae484/GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:03,129] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:03,130] [INFO] Task started: HMMsearch
[2023-06-13 17:12:03,130] [INFO] Running command: hmmsearch --tblout GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/reference_markers.hmm GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:03,420] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:03,423] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9bb3480f-996c-4838-ab23-0f0d073ae484/GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-13 17:12:03,452] [INFO] Query marker FASTA was written to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 17:12:03,453] [INFO] Task started: Blastn
[2023-06-13 17:12:03,453] [INFO] Running command: blastn -query GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/reference_markers.fasta -out GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:04,109] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:04,113] [INFO] Selected 26 target genomes.
[2023-06-13 17:12:04,113] [INFO] Target genome list was writen to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 17:12:04,126] [INFO] Task started: fastANI
[2023-06-13 17:12:04,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb3480f-996c-4838-ab23-0f0d073ae484/GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:21,989] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:21,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:21,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:22,015] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:22,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:22,016] [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
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.1938	115	1007	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	76.7687	116	1007	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.7205	119	1007	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.6762	103	1007	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	76.6729	123	1007	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	76.6595	125	1007	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.6569	111	1007	95	below_threshold
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	76.6518	123	1007	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.6238	112	1007	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.5994	123	1007	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.5808	80	1007	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.4182	116	1007	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.3822	117	1007	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.2258	63	1007	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	76.1694	83	1007	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.1341	63	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	76.0917	51	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.0763	53	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.0708	53	1007	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.0695	52	1007	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.065	52	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:22,019] [INFO] DFAST Taxonomy check result was written to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 17:12:22,020] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:22,020] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:22,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/checkm_data
[2023-06-13 17:12:22,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:22,073] [INFO] Task started: CheckM
[2023-06-13 17:12:22,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 17:12:51,198] [INFO] Task succeeded: CheckM
[2023-06-13 17:12:51,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:12:51,224] [INFO] ===== Completeness check finished =====
[2023-06-13 17:12:51,225] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:12:51,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 17:12:51,226] [INFO] Task started: Blastn
[2023-06-13 17:12:51,226] [INFO] Running command: blastn -query GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d376397-6403-4225-87dd-aa410c715971/dqc_reference/reference_markers_gtdb.fasta -out GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:52,130] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:52,135] [INFO] Selected 18 target genomes.
[2023-06-13 17:12:52,135] [INFO] Target genome list was writen to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:12:52,167] [INFO] Task started: fastANI
[2023-06-13 17:12:52,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb3480f-996c-4838-ab23-0f0d073ae484/GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:01,999] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:02,021] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:13:02,023] [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_018713585.1	s__Pullilachnospira stercoravium	97.9377	726	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	conclusive
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	87.6819	703	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_018711815.1	s__Egerieimonas intestinavium	77.6249	209	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123145.1	s__Oliverpabstia faecicola	77.456	172	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.72	97.58	0.88	0.80	5	-
GCA_000432335.1	s__Oliverpabstia sp000432335	77.4383	182	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.29	99.14	0.86	0.81	5	-
GCA_018374355.1	s__Oliverpabstia sp018374355	77.4188	232	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120315.1	s__Ruminococcus_G avistercoris	77.3022	159	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	99.47	98.95	0.89	0.84	3	-
GCF_009696065.1	s__Oliverpabstia intestinalis	77.2992	152	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCA_017887445.1	s__Fusicatenibacter sp017887445	77.27	174	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716305.1	s__Scatomonas merdigallinarum	77.2457	169	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.11	99.10	0.93	0.92	3	-
GCA_018713515.1	s__Scatomonas pullistercoris	77.0264	166	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.97	99.97	0.94	0.94	2	-
GCA_900552095.1	s__Egerieimonas sp900552095	76.8577	95	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	98.68	98.68	0.68	0.68	2	-
GCF_003885045.1	s__Schaedlerella arabinosiphila	76.6948	104	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.52	96.80	0.74	0.68	10	-
GCA_900542045.1	s__Blautia_A gallistercoris	76.6447	137	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.42	98.42	0.88	0.88	2	-
GCA_019119975.1	s__Blautia merdavium	76.6314	126	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.5838	107	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_019115385.1	s__Mediterraneibacter avicola	76.1737	56	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	76.1131	53	1007	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:02,025] [INFO] GTDB search result was written to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:02,026] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:02,036] [INFO] DFAST_QC result json was written to GCA_930990205.1_ERR3414573_bin.76_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 17:13:02,036] [INFO] DFAST_QC completed!
[2023-06-13 17:13:02,036] [INFO] Total running time: 0h1m8s