[2023-06-13 06:11:18,033] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:18,037] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:18,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference
[2023-06-13 06:11:19,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:19,949] [INFO] Task started: Prodigal
[2023-06-13 06:11:19,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg64ed2130-d988-4294-9a74-02f985f44d54/GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:36,364] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:36,365] [INFO] Task started: HMMsearch
[2023-06-13 06:11:36,365] [INFO] Running command: hmmsearch --tblout GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/reference_markers.hmm GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:36,617] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:36,618] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg64ed2130-d988-4294-9a74-02f985f44d54/GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 06:11:36,649] [INFO] Query marker FASTA was written to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 06:11:36,649] [INFO] Task started: Blastn
[2023-06-13 06:11:36,649] [INFO] Running command: blastn -query GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/reference_markers.fasta -out GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:37,245] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:37,249] [INFO] Selected 13 target genomes.
[2023-06-13 06:11:37,250] [INFO] Target genome list was writen to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 06:11:37,253] [INFO] Task started: fastANI
[2023-06-13 06:11:37,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ed2130-d988-4294-9a74-02f985f44d54/GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:47,414] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:47,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:47,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:47,426] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 06:11:47,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 06:11:47,426] [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
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	98.802	735	890	95	conclusive
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	98.7304	736	890	95	conclusive
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	90.307	686	890	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	81.1186	398	890	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	80.8911	397	890	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	80.8633	396	890	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	80.1168	389	890	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	80.1018	380	890	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.3063	101	890	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	76.9423	97	890	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	76.8391	101	890	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.7088	107	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:11:47,428] [INFO] DFAST Taxonomy check result was written to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 06:11:47,429] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:47,429] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:47,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/checkm_data
[2023-06-13 06:11:47,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:47,473] [INFO] Task started: CheckM
[2023-06-13 06:11:47,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 06:12:36,420] [INFO] Task succeeded: CheckM
[2023-06-13 06:12:36,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:12:36,442] [INFO] ===== Completeness check finished =====
[2023-06-13 06:12:36,443] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:12:36,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 06:12:36,444] [INFO] Task started: Blastn
[2023-06-13 06:12:36,444] [INFO] Running command: blastn -query GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg373cbfe4-c7d2-488b-a452-23abd6226725/dqc_reference/reference_markers_gtdb.fasta -out GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:12:36,892] [INFO] Task succeeded: Blastn
[2023-06-13 06:12:36,897] [INFO] Selected 12 target genomes.
[2023-06-13 06:12:36,897] [INFO] Target genome list was writen to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:12:36,902] [INFO] Task started: fastANI
[2023-06-13 06:12:36,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ed2130-d988-4294-9a74-02f985f44d54/GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:12:46,706] [INFO] Task succeeded: fastANI
[2023-06-13 06:12:46,717] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:12:46,717] [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
GCF_000382445.1	s__Phocaeicola massiliensis	98.7633	735	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	conclusive
GCA_900760795.1	s__Phocaeicola sp900760795	93.4137	540	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493165.1	s__Phocaeicola sp002493165	90.4391	642	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.20	98.75	0.86	0.83	5	-
GCF_013009555.1	s__Phocaeicola dorei	81.0164	405	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCF_000012825.1	s__Phocaeicola vulgatus	80.847	397	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCF_000614185.1	s__Phocaeicola sartorii	80.0929	381	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_011959205.1	s__Phocaeicola sp011959205	79.5001	328	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCA_902388365.1	s__Phocaeicola sp902388365	79.1138	381	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
GCF_000374585.1	s__Phocaeicola barnesiae	76.7293	106	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_000513195.1	s__Bacteroides timonensis	76.686	92	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542985.1	s__Phocaeicola sp900542985	76.3801	96	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_017559935.1	s__Phocaeicola sp017559935	76.2841	72	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:12:46,720] [INFO] GTDB search result was written to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 06:12:46,721] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:12:46,726] [INFO] DFAST_QC result json was written to GCA_947002255.1_SRR19721637_bin.28_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 06:12:46,726] [INFO] DFAST_QC completed!
[2023-06-13 06:12:46,727] [INFO] Total running time: 0h1m29s