[2023-06-29 02:27:46,107] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:27:46,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:27:46,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference
[2023-06-29 02:27:47,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:27:47,311] [INFO] Task started: Prodigal
[2023-06-29 02:27:47,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ac43c8d-9bff-4099-b6f2-406be5038ea0/GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:27:51,046] [INFO] Task succeeded: Prodigal
[2023-06-29 02:27:51,046] [INFO] Task started: HMMsearch
[2023-06-29 02:27:51,047] [INFO] Running command: hmmsearch --tblout GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/reference_markers.hmm GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:27:51,248] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:27:51,250] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ac43c8d-9bff-4099-b6f2-406be5038ea0/GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-29 02:27:51,272] [INFO] Query marker FASTA was written to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 02:27:51,272] [INFO] Task started: Blastn
[2023-06-29 02:27:51,272] [INFO] Running command: blastn -query GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/reference_markers.fasta -out GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:27:51,999] [INFO] Task succeeded: Blastn
[2023-06-29 02:27:52,004] [INFO] Selected 17 target genomes.
[2023-06-29 02:27:52,005] [INFO] Target genome list was writen to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 02:27:52,008] [INFO] Task started: fastANI
[2023-06-29 02:27:52,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac43c8d-9bff-4099-b6f2-406be5038ea0/GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:27:59,610] [INFO] Task succeeded: fastANI
[2023-06-29 02:27:59,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:27:59,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:27:59,623] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:27:59,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:27:59,623] [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
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.4835	145	359	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.1334	111	359	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.0595	118	359	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.0396	117	359	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.0384	101	359	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.9911	108	359	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	77.0072	103	359	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	76.9466	101	359	95	below_threshold
Ruthenibacterium lactatiformans	strain=585-1	GCA_000949455.1	1550024	1550024	suspected-type	True	76.6396	56	359	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:27:59,625] [INFO] DFAST Taxonomy check result was written to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 02:27:59,626] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:27:59,626] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:27:59,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/checkm_data
[2023-06-29 02:27:59,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:27:59,645] [INFO] Task started: CheckM
[2023-06-29 02:27:59,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 02:28:17,531] [INFO] Task succeeded: CheckM
[2023-06-29 02:28:17,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:28:17,555] [INFO] ===== Completeness check finished =====
[2023-06-29 02:28:17,555] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:28:17,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 02:28:17,556] [INFO] Task started: Blastn
[2023-06-29 02:28:17,557] [INFO] Running command: blastn -query GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d94227-c292-4c59-a765-bc187451d6fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:28:18,813] [INFO] Task succeeded: Blastn
[2023-06-29 02:28:18,819] [INFO] Selected 17 target genomes.
[2023-06-29 02:28:18,819] [INFO] Target genome list was writen to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:28:18,827] [INFO] Task started: fastANI
[2023-06-29 02:28:18,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ac43c8d-9bff-4099-b6f2-406be5038ea0/GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:28:25,716] [INFO] Task succeeded: fastANI
[2023-06-29 02:28:25,738] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 02:28:25,738] [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_004555865.1	s__SFJ001 sp004555865	98.5046	330	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	98.44	98.34	0.90	0.89	3	conclusive
GCA_017472375.1	s__SFJ001 sp017472375	80.9356	167	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160955.1	s__Gemmiger_A avium	78.7938	151	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger_A	95.0	98.36	98.15	0.86	0.80	3	-
GCA_019116345.1	s__Fournierella merdipullorum	78.4859	122	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161595.1	s__Fournierella sp002161595	78.4392	150	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
GCA_004558145.1	s__Fournierella excrementavium	78.3786	159	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	97.60	97.45	0.91	0.87	5	-
GCF_002160145.1	s__Fournierella sp002160145	78.3621	150	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.11	98.11	0.91	0.91	2	-
GCA_019118765.1	s__Fournierella merdavium	78.2083	135	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159185.1	s__Fournierella sp002159185	78.1881	143	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112725.1	s__Faecalibacterium intestinipullorum	77.9701	98	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.50	98.50	0.82	0.82	2	-
GCA_019119495.1	s__Gemmiger stercorigallinarum	77.8481	101	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.30	97.15	0.83	0.66	4	-
GCA_019119835.1	s__Gemmiger stercoravium	77.5581	115	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.20	98.14	0.89	0.85	3	-
GCA_002491225.1	s__UBA7177 sp002491225	77.5221	97	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA7177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555405.1	s__Gemmiger sp004555405	77.1319	109	359	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.36	97.23	0.85	0.84	4	-
--------------------------------------------------------------------------------
[2023-06-29 02:28:25,740] [INFO] GTDB search result was written to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 02:28:25,741] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:28:25,745] [INFO] DFAST_QC result json was written to GCA_948468795.1_SRR17622766_bin.2_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 02:28:25,746] [INFO] DFAST_QC completed!
[2023-06-29 02:28:25,746] [INFO] Total running time: 0h0m40s