[2023-06-08 12:54:45,768] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:54:45,772] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:54:45,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference
[2023-06-08 12:54:48,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:54:48,157] [INFO] Task started: Prodigal
[2023-06-08 12:54:48,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a389174-4938-49f3-b2b1-07ed9a963ccc/GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:54:54,297] [INFO] Task succeeded: Prodigal
[2023-06-08 12:54:54,298] [INFO] Task started: HMMsearch
[2023-06-08 12:54:54,298] [INFO] Running command: hmmsearch --tblout GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/reference_markers.hmm GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:54:54,514] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:54:54,516] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a389174-4938-49f3-b2b1-07ed9a963ccc/GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:54:54,543] [INFO] Query marker FASTA was written to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:54:54,544] [INFO] Task started: Blastn
[2023-06-08 12:54:54,544] [INFO] Running command: blastn -query GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/reference_markers.fasta -out GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:54:55,124] [INFO] Task succeeded: Blastn
[2023-06-08 12:54:55,128] [INFO] Selected 13 target genomes.
[2023-06-08 12:54:55,129] [INFO] Target genome list was writen to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:54:55,130] [INFO] Task started: fastANI
[2023-06-08 12:54:55,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a389174-4938-49f3-b2b1-07ed9a963ccc/GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:55:01,235] [INFO] Task succeeded: fastANI
[2023-06-08 12:55:01,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:55:01,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:55:01,249] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:55:01,250] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:55:01,250] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.6094	196	683	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.5233	186	683	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.8625	168	683	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.688	134	683	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.131	55	683	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.1063	120	683	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.7479	76	683	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.425	74	683	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.4085	76	683	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.3916	52	683	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:55:01,252] [INFO] DFAST Taxonomy check result was written to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:55:01,252] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:55:01,253] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:55:01,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/checkm_data
[2023-06-08 12:55:01,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:55:01,280] [INFO] Task started: CheckM
[2023-06-08 12:55:01,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:55:24,330] [INFO] Task succeeded: CheckM
[2023-06-08 12:55:24,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:55:24,353] [INFO] ===== Completeness check finished =====
[2023-06-08 12:55:24,353] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:55:24,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:55:24,354] [INFO] Task started: Blastn
[2023-06-08 12:55:24,354] [INFO] Running command: blastn -query GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf960c4f3-dc63-4a10-baa3-60b94dd7cb16/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:55:25,238] [INFO] Task succeeded: Blastn
[2023-06-08 12:55:25,242] [INFO] Selected 15 target genomes.
[2023-06-08 12:55:25,242] [INFO] Target genome list was writen to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:55:25,244] [INFO] Task started: fastANI
[2023-06-08 12:55:25,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a389174-4938-49f3-b2b1-07ed9a963ccc/GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:55:33,554] [INFO] Task succeeded: fastANI
[2023-06-08 12:55:33,571] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:55:33,572] [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_910575695.1	s__Enterenecus sp910575695	97.9756	609	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585265.1	s__Enterenecus sp910585265	84.471	445	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579595.1	s__Enterenecus sp910579595	84.024	395	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004560375.1	s__Enterenecus sp004560375	83.9872	369	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584285.1	s__Enterenecus sp910584285	83.8414	400	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588495.1	s__Enterenecus sp910588495	83.2536	367	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585155.1	s__Enterenecus sp910585155	83.0564	358	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799475.1	s__Enterenecus sp014799475	82.9697	294	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579155.1	s__Enterenecus sp910579155	82.8238	424	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587285.1	s__Enterenecus sp910587285	82.7107	373	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799565.1	s__Enterenecus sp014799565	82.5509	312	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799485.1	s__Enterenecus sp014799485	82.4864	224	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577525.1	s__Enterenecus sp910577525	82.4273	374	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588135.1	s__Enterenecus sp910588135	82.388	344	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799505.1	s__Enterenecus sp014799505	82.3288	245	683	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:55:33,574] [INFO] GTDB search result was written to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:55:33,574] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:55:33,578] [INFO] DFAST_QC result json was written to GCA_947643485.1_SRR15730543_bin.78_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:55:33,578] [INFO] DFAST_QC completed!
[2023-06-08 12:55:33,578] [INFO] Total running time: 0h0m48s