[2023-06-08 20:04:44,959] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:44,962] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:44,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference
[2023-06-08 20:04:46,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:46,265] [INFO] Task started: Prodigal
[2023-06-08 20:04:46,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cf6889e-eb75-4512-9a4f-81f8e397fe32/GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:56,942] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:56,942] [INFO] Task started: HMMsearch
[2023-06-08 20:04:56,943] [INFO] Running command: hmmsearch --tblout GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/reference_markers.hmm GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:57,250] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:57,252] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6cf6889e-eb75-4512-9a4f-81f8e397fe32/GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:04:57,294] [INFO] Query marker FASTA was written to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:04:57,295] [INFO] Task started: Blastn
[2023-06-08 20:04:57,295] [INFO] Running command: blastn -query GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/reference_markers.fasta -out GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:57,928] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:57,933] [INFO] Selected 23 target genomes.
[2023-06-08 20:04:57,933] [INFO] Target genome list was writen to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:04:57,936] [INFO] Task started: fastANI
[2023-06-08 20:04:57,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf6889e-eb75-4512-9a4f-81f8e397fe32/GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:05:12,535] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:12,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:05:12,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:05:12,542] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:05:12,543] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:05:12,543] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.7687	105	1360	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:05:12,545] [INFO] DFAST Taxonomy check result was written to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:05:12,546] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:05:12,546] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:05:12,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/checkm_data
[2023-06-08 20:05:12,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:05:12,597] [INFO] Task started: CheckM
[2023-06-08 20:05:12,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:05:48,296] [INFO] Task succeeded: CheckM
[2023-06-08 20:05:48,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:05:48,317] [INFO] ===== Completeness check finished =====
[2023-06-08 20:05:48,318] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:05:48,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:05:48,318] [INFO] Task started: Blastn
[2023-06-08 20:05:48,319] [INFO] Running command: blastn -query GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eda96d9-5276-4954-a850-99f107a36e0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:05:49,327] [INFO] Task succeeded: Blastn
[2023-06-08 20:05:49,331] [INFO] Selected 18 target genomes.
[2023-06-08 20:05:49,332] [INFO] Target genome list was writen to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:05:49,337] [INFO] Task started: fastANI
[2023-06-08 20:05:49,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf6889e-eb75-4512-9a4f-81f8e397fe32/GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:06:01,976] [INFO] Task succeeded: fastANI
[2023-06-08 20:06:01,991] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:06:01,992] [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_910587295.1	s__CAG-95 sp910587295	96.3425	1078	1360	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	conclusive
GCA_910585005.1	s__CAG-95 sp910585005	79.8705	450	1360	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	78.4803	263	1360	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_009911035.1	s__CAG-95 sp009911035	78.4192	290	1360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	96.92	95.99	0.83	0.79	4	-
GCA_910579495.1	s__CAG-95 sp910579495	77.9478	263	1360	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_910579425.1	s__CAG-95 sp910579425	77.6326	254	1360	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	77.57	200	1360	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_002490775.1	s__CAG-95 sp002490775	77.4989	157	1360	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_002492465.1	s__CAG-95 sp002492465	77.4094	208	1360	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_009774465.1	s__CAG-95 sp009774465	77.1739	206	1360	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_900553305.1	s__CAG-95 sp900553305	76.8516	79	1360	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-08 20:06:01,994] [INFO] GTDB search result was written to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:06:01,995] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:06:02,001] [INFO] DFAST_QC result json was written to GCA_947175855.1_SRR14411346_bin.9_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:06:02,001] [INFO] DFAST_QC completed!
[2023-06-08 20:06:02,001] [INFO] Total running time: 0h1m17s