[2023-06-05 02:34:33,071] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:34:33,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:34:33,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference
[2023-06-05 02:34:35,947] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:34:35,948] [INFO] Task started: Prodigal
[2023-06-05 02:34:35,948] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2cc8c18-6c28-4a6e-823e-ab0a1f836225/GCA_934293695.1_ERR7738623_bin.286_genomic.fna.gz | prodigal -d GCA_934293695.1_ERR7738623_bin.286_genomic.fna/cds.fna -a GCA_934293695.1_ERR7738623_bin.286_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:34:40,876] [INFO] Task succeeded: Prodigal
[2023-06-05 02:34:40,876] [INFO] Task started: HMMsearch
[2023-06-05 02:34:40,876] [INFO] Running command: hmmsearch --tblout GCA_934293695.1_ERR7738623_bin.286_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/reference_markers.hmm GCA_934293695.1_ERR7738623_bin.286_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:34:41,118] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:34:41,120] [INFO] Found 6/6 markers.
[2023-06-05 02:34:41,146] [INFO] Query marker FASTA was written to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/markers.fasta
[2023-06-05 02:34:41,146] [INFO] Task started: Blastn
[2023-06-05 02:34:41,147] [INFO] Running command: blastn -query GCA_934293695.1_ERR7738623_bin.286_genomic.fna/markers.fasta -db /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/reference_markers.fasta -out GCA_934293695.1_ERR7738623_bin.286_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:34:41,772] [INFO] Task succeeded: Blastn
[2023-06-05 02:34:41,776] [INFO] Selected 25 target genomes.
[2023-06-05 02:34:41,776] [INFO] Target genome list was writen to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/target_genomes.txt
[2023-06-05 02:34:41,806] [INFO] Task started: fastANI
[2023-06-05 02:34:41,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2cc8c18-6c28-4a6e-823e-ab0a1f836225/GCA_934293695.1_ERR7738623_bin.286_genomic.fna.gz --refList GCA_934293695.1_ERR7738623_bin.286_genomic.fna/target_genomes.txt --output GCA_934293695.1_ERR7738623_bin.286_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:34:53,937] [INFO] Task succeeded: fastANI
[2023-06-05 02:34:53,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:34:53,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:34:53,951] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:34:53,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:34:53,951] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.0324	146	648	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.9654	55	648	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	77.8852	57	648	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.406	77	648	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.3953	77	648	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.3197	69	648	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.2813	84	648	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.2589	84	648	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.1418	66	648	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.1406	66	648	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.0672	66	648	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.0044	66	648	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.9664	66	648	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	76.8685	54	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:34:53,954] [INFO] DFAST Taxonomy check result was written to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/tc_result.tsv
[2023-06-05 02:34:53,954] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:34:53,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:34:53,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/checkm_data
[2023-06-05 02:34:53,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:34:53,982] [INFO] Task started: CheckM
[2023-06-05 02:34:53,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293695.1_ERR7738623_bin.286_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293695.1_ERR7738623_bin.286_genomic.fna/checkm_input GCA_934293695.1_ERR7738623_bin.286_genomic.fna/checkm_result
[2023-06-05 02:35:16,195] [INFO] Task succeeded: CheckM
[2023-06-05 02:35:16,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 02:35:16,219] [INFO] ===== Completeness check finished =====
[2023-06-05 02:35:16,219] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:35:16,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293695.1_ERR7738623_bin.286_genomic.fna/markers.fasta)
[2023-06-05 02:35:16,220] [INFO] Task started: Blastn
[2023-06-05 02:35:16,220] [INFO] Running command: blastn -query GCA_934293695.1_ERR7738623_bin.286_genomic.fna/markers.fasta -db /var/lib/cwl/stg2268054f-f6fe-4113-b441-7f97310c8b52/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293695.1_ERR7738623_bin.286_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:35:17,159] [INFO] Task succeeded: Blastn
[2023-06-05 02:35:17,165] [INFO] Selected 20 target genomes.
[2023-06-05 02:35:17,165] [INFO] Target genome list was writen to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:35:17,182] [INFO] Task started: fastANI
[2023-06-05 02:35:17,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2cc8c18-6c28-4a6e-823e-ab0a1f836225/GCA_934293695.1_ERR7738623_bin.286_genomic.fna.gz --refList GCA_934293695.1_ERR7738623_bin.286_genomic.fna/target_genomes_gtdb.txt --output GCA_934293695.1_ERR7738623_bin.286_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:35:26,841] [INFO] Task succeeded: fastANI
[2023-06-05 02:35:26,856] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:35:26,856] [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_900554415.1	s__Bariatricus sp900554415	97.6281	391	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	conclusive
GCA_905216215.1	s__Bariatricus sp905216215	85.4811	421	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	78.294	145	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_004560705.1	s__Bariatricus sp004560705	78.1711	112	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCA_000155875.1	s__Bariatricus comes	78.0662	139	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_001404875.1	s__Dorea_A longicatena_B	77.8156	85	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_000169235.1	s__Dorea formicigenerans	77.3995	75	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_900104635.1	s__Faecalimonas phoceensis	77.3197	69	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	-
GCA_016295505.1	s__Dorea_A sp016295505	77.2307	50	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155205.1	s__Mediterraneibacter lactaris	77.2242	64	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	76.9231	83	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCA_017465565.1	s__Faecalimonas sp017465565	76.9096	69	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550865.1	s__Dorea_A sp900550865	76.7935	80	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203555.1	s__Schaedlerella sp905203555	76.3511	55	648	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:35:26,858] [INFO] GTDB search result was written to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/result_gtdb.tsv
[2023-06-05 02:35:26,859] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:35:26,863] [INFO] DFAST_QC result json was written to GCA_934293695.1_ERR7738623_bin.286_genomic.fna/dqc_result.json
[2023-06-05 02:35:26,863] [INFO] DFAST_QC completed!
[2023-06-05 02:35:26,864] [INFO] Total running time: 0h0m54s