[2023-06-05 23:13:57,068] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:13:57,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:13:57,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference
[2023-06-05 23:13:58,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:13:58,262] [INFO] Task started: Prodigal
[2023-06-05 23:13:58,262] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc2566a0-29d9-4301-8624-1d0709fdca89/GCA_934293955.1_ERR7738265_bin.123_genomic.fna.gz | prodigal -d GCA_934293955.1_ERR7738265_bin.123_genomic.fna/cds.fna -a GCA_934293955.1_ERR7738265_bin.123_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:14:03,001] [INFO] Task succeeded: Prodigal
[2023-06-05 23:14:03,001] [INFO] Task started: HMMsearch
[2023-06-05 23:14:03,001] [INFO] Running command: hmmsearch --tblout GCA_934293955.1_ERR7738265_bin.123_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/reference_markers.hmm GCA_934293955.1_ERR7738265_bin.123_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:14:03,211] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:14:03,212] [INFO] Found 6/6 markers.
[2023-06-05 23:14:03,237] [INFO] Query marker FASTA was written to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/markers.fasta
[2023-06-05 23:14:03,237] [INFO] Task started: Blastn
[2023-06-05 23:14:03,237] [INFO] Running command: blastn -query GCA_934293955.1_ERR7738265_bin.123_genomic.fna/markers.fasta -db /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/reference_markers.fasta -out GCA_934293955.1_ERR7738265_bin.123_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:03,818] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:03,821] [INFO] Selected 23 target genomes.
[2023-06-05 23:14:03,821] [INFO] Target genome list was writen to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/target_genomes.txt
[2023-06-05 23:14:03,822] [INFO] Task started: fastANI
[2023-06-05 23:14:03,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2566a0-29d9-4301-8624-1d0709fdca89/GCA_934293955.1_ERR7738265_bin.123_genomic.fna.gz --refList GCA_934293955.1_ERR7738265_bin.123_genomic.fna/target_genomes.txt --output GCA_934293955.1_ERR7738265_bin.123_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:14:15,868] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:15,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:14:15,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:14:15,891] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:14:15,891] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 23:14:15,891] [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
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	88.4092	399	664	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	79.2308	188	664	95	below_threshold
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	78.3106	138	664	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	77.7885	59	664	95	below_threshold
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	77.7885	59	664	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_000154305.1	105841	105841	type	True	77.6419	58	664	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	77.077	57	664	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.6619	51	664	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.6463	60	664	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.634	55	664	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 23:14:15,893] [INFO] DFAST Taxonomy check result was written to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/tc_result.tsv
[2023-06-05 23:14:15,894] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:14:15,894] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:14:15,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/checkm_data
[2023-06-05 23:14:15,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:14:15,937] [INFO] Task started: CheckM
[2023-06-05 23:14:15,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293955.1_ERR7738265_bin.123_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293955.1_ERR7738265_bin.123_genomic.fna/checkm_input GCA_934293955.1_ERR7738265_bin.123_genomic.fna/checkm_result
[2023-06-05 23:14:35,771] [INFO] Task succeeded: CheckM
[2023-06-05 23:14:35,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:14:35,788] [INFO] ===== Completeness check finished =====
[2023-06-05 23:14:35,788] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:14:35,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293955.1_ERR7738265_bin.123_genomic.fna/markers.fasta)
[2023-06-05 23:14:35,788] [INFO] Task started: Blastn
[2023-06-05 23:14:35,788] [INFO] Running command: blastn -query GCA_934293955.1_ERR7738265_bin.123_genomic.fna/markers.fasta -db /var/lib/cwl/stg77a1d520-30e7-4cc9-9718-1b7ad09c7ee7/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293955.1_ERR7738265_bin.123_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:36,747] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:36,750] [INFO] Selected 10 target genomes.
[2023-06-05 23:14:36,750] [INFO] Target genome list was writen to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:14:36,793] [INFO] Task started: fastANI
[2023-06-05 23:14:36,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc2566a0-29d9-4301-8624-1d0709fdca89/GCA_934293955.1_ERR7738265_bin.123_genomic.fna.gz --refList GCA_934293955.1_ERR7738265_bin.123_genomic.fna/target_genomes_gtdb.txt --output GCA_934293955.1_ERR7738265_bin.123_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:14:41,086] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:41,092] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:14:41,092] [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
GCF_001404655.1	s__Anaerostipes hadrus_A	98.4395	456	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	conclusive
GCA_902362875.1	s__Anaerostipes sp900066705	91.1255	445	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCF_000332875.2	s__Anaerostipes hadrus	88.4092	399	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.35	97.09	0.85	0.65	78	-
GCA_905215045.1	s__Anaerostipes sp905215045	87.7766	301	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918155.1	s__Anaerostipes sp018918155	80.2645	223	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940315.1	s__Anaerostipes sp001940315	79.2924	188	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.20	99.20	0.89	0.89	2	-
GCA_900756035.1	s__Anaerostipes sp900756035	78.7612	172	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119895.1	s__Anaerostipes avistercoris	78.3462	146	664	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:14:41,094] [INFO] GTDB search result was written to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/result_gtdb.tsv
[2023-06-05 23:14:41,094] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:14:41,097] [INFO] DFAST_QC result json was written to GCA_934293955.1_ERR7738265_bin.123_genomic.fna/dqc_result.json
[2023-06-05 23:14:41,097] [INFO] DFAST_QC completed!
[2023-06-05 23:14:41,097] [INFO] Total running time: 0h0m44s