[2023-06-30 17:00:13,414] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:13,417] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:13,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference
[2023-06-30 17:00:14,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:14,871] [INFO] Task started: Prodigal
[2023-06-30 17:00:14,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ec051ef-521b-42a4-83fe-d81a108b282d/GCA_900757095.1_ERS537270_10_genomic.fna.gz | prodigal -d GCA_900757095.1_ERS537270_10_genomic.fna/cds.fna -a GCA_900757095.1_ERS537270_10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:21,471] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:21,471] [INFO] Task started: HMMsearch
[2023-06-30 17:00:21,471] [INFO] Running command: hmmsearch --tblout GCA_900757095.1_ERS537270_10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/reference_markers.hmm GCA_900757095.1_ERS537270_10_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:21,739] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:21,741] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg9ec051ef-521b-42a4-83fe-d81a108b282d/GCA_900757095.1_ERS537270_10_genomic.fna.gz]
[2023-06-30 17:00:21,773] [INFO] Query marker FASTA was written to GCA_900757095.1_ERS537270_10_genomic.fna/markers.fasta
[2023-06-30 17:00:21,774] [INFO] Task started: Blastn
[2023-06-30 17:00:21,774] [INFO] Running command: blastn -query GCA_900757095.1_ERS537270_10_genomic.fna/markers.fasta -db /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/reference_markers.fasta -out GCA_900757095.1_ERS537270_10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:22,358] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:22,363] [INFO] Selected 15 target genomes.
[2023-06-30 17:00:22,363] [INFO] Target genome list was writen to GCA_900757095.1_ERS537270_10_genomic.fna/target_genomes.txt
[2023-06-30 17:00:22,364] [INFO] Task started: fastANI
[2023-06-30 17:00:22,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ec051ef-521b-42a4-83fe-d81a108b282d/GCA_900757095.1_ERS537270_10_genomic.fna.gz --refList GCA_900757095.1_ERS537270_10_genomic.fna/target_genomes.txt --output GCA_900757095.1_ERS537270_10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:30,217] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:30,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:30,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:30,235] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:30,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:00:30,236] [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
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	91.4713	128	756	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	91.2426	130	756	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	89.1414	83	756	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	84.5397	101	756	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	82.6825	58	756	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	82.2812	69	756	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	82.0551	68	756	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.8562	75	756	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	81.4614	65	756	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	81.2976	68	756	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.0956	52	756	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	80.9521	62	756	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	80.1638	62	756	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.6617	70	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:00:30,238] [INFO] DFAST Taxonomy check result was written to GCA_900757095.1_ERS537270_10_genomic.fna/tc_result.tsv
[2023-06-30 17:00:30,239] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:30,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:30,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/checkm_data
[2023-06-30 17:00:30,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:30,282] [INFO] Task started: CheckM
[2023-06-30 17:00:30,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900757095.1_ERS537270_10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900757095.1_ERS537270_10_genomic.fna/checkm_input GCA_900757095.1_ERS537270_10_genomic.fna/checkm_result
[2023-06-30 17:00:58,179] [INFO] Task succeeded: CheckM
[2023-06-30 17:00:58,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.96%
Contamintation: 12.84%
Strain heterogeneity: 23.08%
--------------------------------------------------------------------------------
[2023-06-30 17:00:58,211] [INFO] ===== Completeness check finished =====
[2023-06-30 17:00:58,212] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:00:58,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900757095.1_ERS537270_10_genomic.fna/markers.fasta)
[2023-06-30 17:00:58,213] [INFO] Task started: Blastn
[2023-06-30 17:00:58,213] [INFO] Running command: blastn -query GCA_900757095.1_ERS537270_10_genomic.fna/markers.fasta -db /var/lib/cwl/stg02016465-cee4-43c6-b003-822d9eb8717e/dqc_reference/reference_markers_gtdb.fasta -out GCA_900757095.1_ERS537270_10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:59,012] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:59,018] [INFO] Selected 19 target genomes.
[2023-06-30 17:00:59,018] [INFO] Target genome list was writen to GCA_900757095.1_ERS537270_10_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:00:59,027] [INFO] Task started: fastANI
[2023-06-30 17:00:59,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ec051ef-521b-42a4-83fe-d81a108b282d/GCA_900757095.1_ERS537270_10_genomic.fna.gz --refList GCA_900757095.1_ERS537270_10_genomic.fna/target_genomes_gtdb.txt --output GCA_900757095.1_ERS537270_10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:08,599] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:08,610] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 17:01:08,611] [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_001312505.1	s__Mediterraneibacter faecis	92.088	135	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_000484655.1	s__Blautia_A wexlerae	91.4713	128	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_013300825.1	s__Blautia_A wexlerae_B	89.276	113	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_000174195.1	s__Roseburia inulinivorans	89.1414	83	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCF_003471165.1	s__Blautia_A sp003471165	86.8299	116	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_018919065.1	s__Blautia_A sp018919065	85.4011	97	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155875.1	s__Bariatricus comes	82.1263	72	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_905209435.1	s__Blautia_A sp905209435	82.0114	80	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	81.9689	74	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCF_013304825.1	s__Blautia_A schinkii	81.3779	68	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCF_900537995.1	s__Roseburia intestinalis	81.3546	66	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_000155205.1	s__Mediterraneibacter lactaris	79.6371	70	756	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_003470905.1	s__Roseburia sp003470905	79.0933	57	756	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
--------------------------------------------------------------------------------
[2023-06-30 17:01:08,613] [INFO] GTDB search result was written to GCA_900757095.1_ERS537270_10_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:08,613] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:08,617] [INFO] DFAST_QC result json was written to GCA_900757095.1_ERS537270_10_genomic.fna/dqc_result.json
[2023-06-30 17:01:08,618] [INFO] DFAST_QC completed!
[2023-06-30 17:01:08,618] [INFO] Total running time: 0h0m55s