[2023-06-19 08:51:51,640] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:51:51,643] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:51:51,643] [INFO] DQC Reference Directory: /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference
[2023-06-19 08:51:53,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:51:53,919] [INFO] Task started: Prodigal
[2023-06-19 08:51:53,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgda7cd9f6-725f-4406-add7-688a50017e1e/GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:52:05,612] [INFO] Task succeeded: Prodigal
[2023-06-19 08:52:05,612] [INFO] Task started: HMMsearch
[2023-06-19 08:52:05,613] [INFO] Running command: hmmsearch --tblout GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/reference_markers.hmm GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:52:05,912] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:52:05,914] [INFO] Found 6/6 markers.
[2023-06-19 08:52:05,965] [INFO] Query marker FASTA was written to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 08:52:05,965] [INFO] Task started: Blastn
[2023-06-19 08:52:05,965] [INFO] Running command: blastn -query GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/reference_markers.fasta -out GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:52:06,673] [INFO] Task succeeded: Blastn
[2023-06-19 08:52:06,677] [INFO] Selected 28 target genomes.
[2023-06-19 08:52:06,677] [INFO] Target genome list was writen to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 08:52:06,679] [INFO] Task started: fastANI
[2023-06-19 08:52:06,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7cd9f6-725f-4406-add7-688a50017e1e/GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:52:27,940] [INFO] Task succeeded: fastANI
[2023-06-19 08:52:27,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:52:27,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:52:27,950] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:52:27,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:52:27,950] [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
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	76.582	64	1096	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	76.1349	80	1096	95	below_threshold
Desulfoferrobacter suflitae	strain=DRH4	GCA_022603395.1	2865782	2865782	type	True	76.1159	50	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:52:27,952] [INFO] DFAST Taxonomy check result was written to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 08:52:27,953] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:52:27,953] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:52:27,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/checkm_data
[2023-06-19 08:52:27,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:52:28,017] [INFO] Task started: CheckM
[2023-06-19 08:52:28,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 08:53:06,388] [INFO] Task succeeded: CheckM
[2023-06-19 08:53:06,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 8.68%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:53:06,422] [INFO] ===== Completeness check finished =====
[2023-06-19 08:53:06,423] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:53:06,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 08:53:06,424] [INFO] Task started: Blastn
[2023-06-19 08:53:06,424] [INFO] Running command: blastn -query GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc951124b-5a77-456f-b78f-f282f8d59273/dqc_reference/reference_markers_gtdb.fasta -out GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:53:07,507] [INFO] Task succeeded: Blastn
[2023-06-19 08:53:07,511] [INFO] Selected 27 target genomes.
[2023-06-19 08:53:07,511] [INFO] Target genome list was writen to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:53:07,522] [INFO] Task started: fastANI
[2023-06-19 08:53:07,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgda7cd9f6-725f-4406-add7-688a50017e1e/GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:53:24,065] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:24,075] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:53:24,076] [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_011328915.1	s__DSUX01 sp011328915	76.7765	124	1096	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__DSUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014965.1	s__Syntrophobacter fumaroxidans	76.582	64	1096	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__Syntrophobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359885.1	s__Desulfacinum sp014359885	76.1703	81	1096	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517775.1	s__JAAYUJ01 sp012517775	75.9581	51	1096	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAAYUJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329395.1	s__Desulfosoma infernum_A	75.8113	56	1096	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:53:24,078] [INFO] GTDB search result was written to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 08:53:24,079] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:53:24,082] [INFO] DFAST_QC result json was written to GCA_937889795.1_SRR3330210_bin.4_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 08:53:24,082] [INFO] DFAST_QC completed!
[2023-06-19 08:53:24,082] [INFO] Total running time: 0h1m32s