[2023-06-13 02:18:23,039] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:18:23,043] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:18:23,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference
[2023-06-13 02:18:24,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:18:24,666] [INFO] Task started: Prodigal
[2023-06-13 02:18:24,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg762c9e2e-d7d0-4ac4-89e1-cb73aed8ad01/GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:18:31,763] [INFO] Task succeeded: Prodigal
[2023-06-13 02:18:31,763] [INFO] Task started: HMMsearch
[2023-06-13 02:18:31,763] [INFO] Running command: hmmsearch --tblout GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/reference_markers.hmm GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:18:32,078] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:18:32,081] [INFO] Found 6/6 markers.
[2023-06-13 02:18:32,122] [INFO] Query marker FASTA was written to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 02:18:32,122] [INFO] Task started: Blastn
[2023-06-13 02:18:32,122] [INFO] Running command: blastn -query GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/reference_markers.fasta -out GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:18:32,797] [INFO] Task succeeded: Blastn
[2023-06-13 02:18:32,800] [INFO] Selected 30 target genomes.
[2023-06-13 02:18:32,801] [INFO] Target genome list was writen to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:18:32,804] [INFO] Task started: fastANI
[2023-06-13 02:18:32,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg762c9e2e-d7d0-4ac4-89e1-cb73aed8ad01/GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:18:48,084] [INFO] Task succeeded: fastANI
[2023-06-13 02:18:48,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:18:48,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:18:48,087] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:18:48,087] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:18:48,087] [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
--------------------------------------------------------------------------------
[2023-06-13 02:18:48,089] [INFO] DFAST Taxonomy check result was written to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:18:48,090] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:18:48,090] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:18:48,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/checkm_data
[2023-06-13 02:18:48,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:18:48,128] [INFO] Task started: CheckM
[2023-06-13 02:18:48,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 02:19:16,148] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:16,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:16,172] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:16,172] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:16,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:19:16,173] [INFO] Task started: Blastn
[2023-06-13 02:19:16,173] [INFO] Running command: blastn -query GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg55599f86-d73f-4653-b31c-02303485802f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:16,967] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:16,971] [INFO] Selected 15 target genomes.
[2023-06-13 02:19:16,972] [INFO] Target genome list was writen to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:16,980] [INFO] Task started: fastANI
[2023-06-13 02:19:16,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg762c9e2e-d7d0-4ac4-89e1-cb73aed8ad01/GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:24,068] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:24,084] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:19:24,084] [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_910585605.1	s__CAG-590 sp910585605	78.8171	296	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544905.1	s__CAG-590 sp900544905	78.4	291	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	99.91	99.86	0.94	0.93	3	-
GCA_900548855.1	s__CAG-590 sp900548855	78.2835	297	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	99.80	99.61	0.88	0.84	3	-
GCA_910584695.1	s__CAG-590 sp910584695	78.1487	222	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431135.1	s__CAG-590 sp000431135	78.0874	142	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	98.51	98.51	0.89	0.89	3	-
GCA_900769115.1	s__CAG-590 sp900769115	78.0252	132	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	96.22	96.22	0.85	0.85	2	-
GCA_015057435.1	s__CAG-590 sp015057435	77.9274	137	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395635.1	s__CAG-590 sp017395635	77.8897	142	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552885.1	s__CAG-590 sp900552885	77.7193	99	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	97.66	97.66	0.76	0.76	2	-
GCA_017479085.1	s__CAG-590 sp017479085	77.0813	117	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470935.1	s__CAG-590 sp017470935	77.0101	84	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236365.1	s__CAG-590 sp905236365	76.9997	99	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623675.1	s__CAG-632 sp017623675	76.981	62	958	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-632	95.0	97.84	97.84	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:24,086] [INFO] GTDB search result was written to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:24,087] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:24,090] [INFO] DFAST_QC result json was written to GCA_947178475.1_SRR14411261_bin.12_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:19:24,090] [INFO] DFAST_QC completed!
[2023-06-13 02:19:24,090] [INFO] Total running time: 0h1m1s