[2023-06-19 02:24:58,964] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:24:58,966] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:24:58,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference
[2023-06-19 02:25:00,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:00,195] [INFO] Task started: Prodigal
[2023-06-19 02:25:00,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f4a7700-d6ca-4033-b33f-34dbedd31f9c/GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:12,417] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:12,417] [INFO] Task started: HMMsearch
[2023-06-19 02:25:12,417] [INFO] Running command: hmmsearch --tblout GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/reference_markers.hmm GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:12,663] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:12,665] [INFO] Found 6/6 markers.
[2023-06-19 02:25:12,692] [INFO] Query marker FASTA was written to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 02:25:12,693] [INFO] Task started: Blastn
[2023-06-19 02:25:12,693] [INFO] Running command: blastn -query GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/reference_markers.fasta -out GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:13,282] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:13,286] [INFO] Selected 24 target genomes.
[2023-06-19 02:25:13,286] [INFO] Target genome list was writen to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 02:25:13,288] [INFO] Task started: fastANI
[2023-06-19 02:25:13,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f4a7700-d6ca-4033-b33f-34dbedd31f9c/GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:28,887] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:28,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:28,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:28,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:28,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:25:28,890] [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
--------------------------------------------------------------------------------
[2023-06-19 02:25:28,892] [INFO] DFAST Taxonomy check result was written to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 02:25:28,893] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:28,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:28,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/checkm_data
[2023-06-19 02:25:28,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:28,923] [INFO] Task started: CheckM
[2023-06-19 02:25:28,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 02:26:08,288] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:08,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:08,310] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:08,310] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:08,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 02:26:08,311] [INFO] Task started: Blastn
[2023-06-19 02:26:08,311] [INFO] Running command: blastn -query GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f071760-2c2a-4fc7-984b-87437ac56941/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:09,097] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:09,101] [INFO] Selected 15 target genomes.
[2023-06-19 02:26:09,102] [INFO] Target genome list was writen to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:09,145] [INFO] Task started: fastANI
[2023-06-19 02:26:09,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f4a7700-d6ca-4033-b33f-34dbedd31f9c/GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:16,450] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:16,470] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 02:26:16,470] [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_902787095.1	s__Limimorpha sp902787095	81.8243	371	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.76	97.57	0.85	0.76	4	-
GCA_900315175.1	s__Limimorpha sp900315175	81.6986	462	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	98.94	98.39	0.95	0.92	4	-
GCA_905236635.1	s__Limimorpha sp905236635	81.4982	401	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.38	97.38	0.87	0.87	2	-
GCA_902774295.1	s__Limimorpha sp902774295	81.4943	460	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.98	96.75	0.92	0.89	3	-
GCA_002311655.1	s__Limimorpha sp002311655	81.3014	437	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645275.1	s__Limimorpha sp017645275	81.2306	367	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.51	96.51	0.76	0.76	2	-
GCA_001603665.1	s__Limimorpha sp001603665	81.2144	401	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234275.1	s__Limimorpha sp905234275	81.2055	443	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.78	96.78	0.93	0.93	2	-
GCA_017649945.1	s__Limimorpha sp017649945	81.1237	360	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	98.04	97.49	0.83	0.78	3	-
GCA_017553625.1	s__Limimorpha sp017553625	81.0544	402	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538795.1	s__Limimorpha sp017538795	80.8725	411	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542475.1	s__Limimorpha sp900542475	80.1868	366	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	99.94	99.94	0.95	0.95	2	-
GCA_016282015.1	s__Limimorpha sp016282015	79.6627	351	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769875.1	s__Limimorpha sp902769875	77.373	89	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769815.1	s__Limimorpha sp902769815	76.6681	86	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:16,472] [INFO] GTDB search result was written to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:16,473] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:16,476] [INFO] DFAST_QC result json was written to GCA_937906455.1_ERR1278105_bin.52_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 02:26:16,476] [INFO] DFAST_QC completed!
[2023-06-19 02:26:16,476] [INFO] Total running time: 0h1m18s