[2023-06-29 01:21:37,970] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:21:37,972] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:21:37,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference
[2023-06-29 01:21:39,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:21:39,451] [INFO] Task started: Prodigal
[2023-06-29 01:21:39,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dc9e7cb-0310-46a4-b072-e1808fd3a924/GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:21:41,775] [INFO] Task succeeded: Prodigal
[2023-06-29 01:21:41,776] [INFO] Task started: HMMsearch
[2023-06-29 01:21:41,776] [INFO] Running command: hmmsearch --tblout GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/reference_markers.hmm GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:21:42,014] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:21:42,015] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6dc9e7cb-0310-46a4-b072-e1808fd3a924/GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-29 01:21:42,034] [INFO] Query marker FASTA was written to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 01:21:42,035] [INFO] Task started: Blastn
[2023-06-29 01:21:42,035] [INFO] Running command: blastn -query GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/reference_markers.fasta -out GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:21:42,640] [INFO] Task succeeded: Blastn
[2023-06-29 01:21:42,645] [INFO] Selected 20 target genomes.
[2023-06-29 01:21:42,646] [INFO] Target genome list was writen to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 01:21:42,648] [INFO] Task started: fastANI
[2023-06-29 01:21:42,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc9e7cb-0310-46a4-b072-e1808fd3a924/GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:21:54,030] [INFO] Task succeeded: fastANI
[2023-06-29 01:21:54,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:21:54,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:21:54,037] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:21:54,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:21:54,037] [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
Clostridium sporogenes	strain=ATCC 3584	GCA_002008145.1	1509	1509	type	True	74.9088	50	441	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	74.9088	50	441	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	74.9088	50	441	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	74.8896	52	441	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:21:54,039] [INFO] DFAST Taxonomy check result was written to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 01:21:54,040] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:21:54,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:21:54,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/checkm_data
[2023-06-29 01:21:54,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:21:54,061] [INFO] Task started: CheckM
[2023-06-29 01:21:54,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 01:22:10,139] [INFO] Task succeeded: CheckM
[2023-06-29 01:22:10,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:22:10,164] [INFO] ===== Completeness check finished =====
[2023-06-29 01:22:10,165] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:22:10,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 01:22:10,166] [INFO] Task started: Blastn
[2023-06-29 01:22:10,166] [INFO] Running command: blastn -query GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ea70af-e86b-4f35-9707-fc2618dd550a/dqc_reference/reference_markers_gtdb.fasta -out GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:22:10,957] [INFO] Task succeeded: Blastn
[2023-06-29 01:22:10,961] [INFO] Selected 10 target genomes.
[2023-06-29 01:22:10,961] [INFO] Target genome list was writen to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:22:10,964] [INFO] Task started: fastANI
[2023-06-29 01:22:10,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc9e7cb-0310-46a4-b072-e1808fd3a924/GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:22:13,944] [INFO] Task succeeded: fastANI
[2023-06-29 01:22:13,954] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:22:13,954] [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_000438255.1	s__CAG-269 sp000438255	81.7192	196	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_900551615.1	s__CAG-269 sp900551615	81.7173	209	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_900753165.1	s__CAG-269 sp900753165	81.7004	177	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.76	0.76	2	-
GCA_900552555.1	s__CAG-269 sp900552555	81.6341	217	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001916005.1	s__CAG-269 sp001916005	81.5018	207	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_001916065.1	s__CAG-269 sp001916065	81.4394	207	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.24	97.60	0.86	0.82	5	-
GCA_000435535.1	s__CAG-269 sp000435535	80.634	194	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.79	0.79	2	-
GCA_017613275.1	s__CAG-269 sp017613275	78.0488	98	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430135.1	s__CAG-269 sp017430135	77.8625	143	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001915925.1	s__Merdicola sp001915925	77.6876	83	441	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Merdicola	95.0	97.40	96.53	0.88	0.85	5	-
--------------------------------------------------------------------------------
[2023-06-29 01:22:13,956] [INFO] GTDB search result was written to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 01:22:13,956] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:22:13,959] [INFO] DFAST_QC result json was written to GCA_948436985.1_SRR17684637_bin.74_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 01:22:13,960] [INFO] DFAST_QC completed!
[2023-06-29 01:22:13,960] [INFO] Total running time: 0h0m36s