[2023-06-08 03:42:22,954] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,956] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference
[2023-06-08 03:42:24,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:24,316] [INFO] Task started: Prodigal
[2023-06-08 03:42:24,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dfeb672-9a8c-42a9-b431-46b00fb7a912/GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:29,499] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:29,500] [INFO] Task started: HMMsearch
[2023-06-08 03:42:29,500] [INFO] Running command: hmmsearch --tblout GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/reference_markers.hmm GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:29,741] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:29,742] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5dfeb672-9a8c-42a9-b431-46b00fb7a912/GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 03:42:29,767] [INFO] Query marker FASTA was written to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:42:29,767] [INFO] Task started: Blastn
[2023-06-08 03:42:29,768] [INFO] Running command: blastn -query GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/reference_markers.fasta -out GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:30,255] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:30,259] [INFO] Selected 13 target genomes.
[2023-06-08 03:42:30,259] [INFO] Target genome list was writen to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:42:30,261] [INFO] Task started: fastANI
[2023-06-08 03:42:30,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dfeb672-9a8c-42a9-b431-46b00fb7a912/GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:36,838] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:36,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:36,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:36,841] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:36,841] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:42:36,841] [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
--------------------------------------------------------------------------------
[2023-06-08 03:42:36,847] [INFO] DFAST Taxonomy check result was written to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:42:36,847] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:42:36,848] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:42:36,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/checkm_data
[2023-06-08 03:42:36,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:42:36,882] [INFO] Task started: CheckM
[2023-06-08 03:42:36,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:42:59,585] [INFO] Task succeeded: CheckM
[2023-06-08 03:42:59,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:42:59,630] [INFO] ===== Completeness check finished =====
[2023-06-08 03:42:59,630] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:42:59,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:42:59,631] [INFO] Task started: Blastn
[2023-06-08 03:42:59,631] [INFO] Running command: blastn -query GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg540a7b52-526d-4e28-a048-61be96cdf876/dqc_reference/reference_markers_gtdb.fasta -out GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:00,110] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:00,115] [INFO] Selected 11 target genomes.
[2023-06-08 03:43:00,115] [INFO] Target genome list was writen to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:43:00,118] [INFO] Task started: fastANI
[2023-06-08 03:43:00,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dfeb672-9a8c-42a9-b431-46b00fb7a912/GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:43:06,820] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:06,834] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:43:06,834] [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_000403495.2	s__CAG-95 sp000403495	98.6069	618	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	conclusive
GCA_009774465.1	s__CAG-95 sp009774465	87.7415	525	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.09	98.09	0.83	0.83	2	-
GCA_002490775.1	s__CAG-95 sp002490775	85.7527	452	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804245.1	s__CAG-95 sp014804245	78.4787	118	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917485.1	s__CAG-95 sp009917485	78.3188	194	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804785.1	s__CAG-95 sp014804785	77.9255	200	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587295.1	s__CAG-95 sp910587295	77.6153	124	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804285.1	s__CAG-95 sp014804285	76.7203	116	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585715.1	s__RGIG3040 sp910585715	76.242	62	679	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:43:06,836] [INFO] GTDB search result was written to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:43:06,837] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:43:06,840] [INFO] DFAST_QC result json was written to GCA_947369435.1_SRR16348858_bin.2_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:43:06,841] [INFO] DFAST_QC completed!
[2023-06-08 03:43:06,841] [INFO] Total running time: 0h0m44s