[2023-06-28 20:40:49,632] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:40:49,634] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:40:49,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference
[2023-06-28 20:40:50,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:40:50,891] [INFO] Task started: Prodigal
[2023-06-28 20:40:50,891] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ebc167-eeba-4252-aca5-0b9c38964a52/GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:40:55,107] [INFO] Task succeeded: Prodigal
[2023-06-28 20:40:55,107] [INFO] Task started: HMMsearch
[2023-06-28 20:40:55,107] [INFO] Running command: hmmsearch --tblout GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/reference_markers.hmm GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:40:55,354] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:40:55,356] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf8ebc167-eeba-4252-aca5-0b9c38964a52/GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-28 20:40:55,381] [INFO] Query marker FASTA was written to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 20:40:55,382] [INFO] Task started: Blastn
[2023-06-28 20:40:55,382] [INFO] Running command: blastn -query GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/reference_markers.fasta -out GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:40:55,972] [INFO] Task succeeded: Blastn
[2023-06-28 20:40:55,977] [INFO] Selected 18 target genomes.
[2023-06-28 20:40:55,977] [INFO] Target genome list was writen to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 20:40:55,979] [INFO] Task started: fastANI
[2023-06-28 20:40:55,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ebc167-eeba-4252-aca5-0b9c38964a52/GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:04,704] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:04,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:04,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:04,723] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 20:41:04,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 20:41:04,723] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	99.1236	535	552	95	conclusive
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.4002	155	552	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.3567	160	552	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	77.3483	107	552	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.1965	117	552	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.1732	116	552	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.1626	115	552	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.0238	122	552	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	76.8782	83	552	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	76.8467	80	552	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	76.7382	68	552	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.6744	86	552	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.5509	75	552	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.5467	73	552	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	75.6776	55	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:41:04,725] [INFO] DFAST Taxonomy check result was written to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 20:41:04,725] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:04,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:04,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/checkm_data
[2023-06-28 20:41:04,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:04,751] [INFO] Task started: CheckM
[2023-06-28 20:41:04,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 20:41:25,031] [INFO] Task succeeded: CheckM
[2023-06-28 20:41:25,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:41:25,055] [INFO] ===== Completeness check finished =====
[2023-06-28 20:41:25,056] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:41:25,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 20:41:25,056] [INFO] Task started: Blastn
[2023-06-28 20:41:25,057] [INFO] Running command: blastn -query GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg184c8260-635e-4dde-898f-fe93f4f68383/dqc_reference/reference_markers_gtdb.fasta -out GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:25,903] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:25,908] [INFO] Selected 14 target genomes.
[2023-06-28 20:41:25,908] [INFO] Target genome list was writen to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:41:25,915] [INFO] Task started: fastANI
[2023-06-28 20:41:25,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ebc167-eeba-4252-aca5-0b9c38964a52/GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:41:33,435] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:33,446] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 20:41:33,446] [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_000155875.1	s__Bariatricus comes	98.9432	520	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	inconclusive
GCF_013300725.1	s__Bariatricus comes_A	95.7639	521	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	inconclusive
GCA_001312505.1	s__Mediterraneibacter faecis	78.3801	133	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCA_004560705.1	s__Bariatricus sp004560705	78.1824	170	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCF_003435815.1	s__CAG-317 sp000433215	77.3732	142	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_900086725.1	s__Bariatricus massiliensis	77.3483	107	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	77.1965	117	552	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	-
GCF_014287635.1	s__1XD42-69 sp014287635	77.1704	60	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCA_003480425.1	s__Schaedlerella sp900066545	77.1267	91	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCF_016900655.1	s__Sellimonas avistercoris	76.8911	104	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	98.38	98.11	0.87	0.78	13	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	76.4994	62	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119995.1	s__Mediterraneibacter faecavium	76.2249	60	552	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-28 20:41:33,448] [INFO] GTDB search result was written to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 20:41:33,449] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:41:33,453] [INFO] DFAST_QC result json was written to GCA_948472445.1_SRR17622767_bin.63_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 20:41:33,453] [INFO] DFAST_QC completed!
[2023-06-28 20:41:33,454] [INFO] Total running time: 0h0m44s