[2023-06-17 16:01:46,523] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:01:46,527] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:01:46,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference
[2023-06-17 16:01:47,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:01:47,865] [INFO] Task started: Prodigal
[2023-06-17 16:01:47,866] [INFO] Running command: gunzip -c /var/lib/cwl/stgfec94bc5-8107-421a-98af-8aa409b07e64/GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna.gz | prodigal -d GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/cds.fna -a GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:01:52,531] [INFO] Task succeeded: Prodigal
[2023-06-17 16:01:52,531] [INFO] Task started: HMMsearch
[2023-06-17 16:01:52,532] [INFO] Running command: hmmsearch --tblout GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/reference_markers.hmm GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:01:52,774] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:01:52,776] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfec94bc5-8107-421a-98af-8aa409b07e64/GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna.gz]
[2023-06-17 16:01:52,808] [INFO] Query marker FASTA was written to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/markers.fasta
[2023-06-17 16:01:52,809] [INFO] Task started: Blastn
[2023-06-17 16:01:52,809] [INFO] Running command: blastn -query GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/reference_markers.fasta -out GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:01:53,548] [INFO] Task succeeded: Blastn
[2023-06-17 16:01:53,553] [INFO] Selected 16 target genomes.
[2023-06-17 16:01:53,554] [INFO] Target genome list was writen to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/target_genomes.txt
[2023-06-17 16:01:53,556] [INFO] Task started: fastANI
[2023-06-17 16:01:53,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec94bc5-8107-421a-98af-8aa409b07e64/GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna.gz --refList GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/target_genomes.txt --output GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:02:00,425] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:00,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:02:00,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:02:00,437] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:02:00,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:02:00,438] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.9123	207	543	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.6113	164	543	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4302	81	543	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3079	110	543	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.3056	84	543	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.199	81	543	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.1044	110	543	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.9936	54	543	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.6333	62	543	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:02:00,440] [INFO] DFAST Taxonomy check result was written to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/tc_result.tsv
[2023-06-17 16:02:00,441] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:02:00,441] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:02:00,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/checkm_data
[2023-06-17 16:02:00,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:02:00,470] [INFO] Task started: CheckM
[2023-06-17 16:02:00,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/checkm_input GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/checkm_result
[2023-06-17 16:02:20,756] [INFO] Task succeeded: CheckM
[2023-06-17 16:02:20,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:02:20,783] [INFO] ===== Completeness check finished =====
[2023-06-17 16:02:20,783] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:02:20,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/markers.fasta)
[2023-06-17 16:02:20,784] [INFO] Task started: Blastn
[2023-06-17 16:02:20,784] [INFO] Running command: blastn -query GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stg6974e6d3-a727-4cc4-a95c-87545d954c0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:02:22,053] [INFO] Task succeeded: Blastn
[2023-06-17 16:02:22,060] [INFO] Selected 21 target genomes.
[2023-06-17 16:02:22,060] [INFO] Target genome list was writen to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:02:22,120] [INFO] Task started: fastANI
[2023-06-17 16:02:22,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec94bc5-8107-421a-98af-8aa409b07e64/GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna.gz --refList GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/target_genomes_gtdb.txt --output GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:02:29,570] [INFO] Task succeeded: fastANI
[2023-06-17 16:02:29,593] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:02:29,593] [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_900552475.1	s__CAG-83 sp900552475	99.2878	459	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.74	98.42	0.88	0.85	4	conclusive
GCA_900545495.1	s__CAG-83 sp900545495	79.8575	213	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900551355.1	s__CAG-83 sp900551355	79.7236	191	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900547745.1	s__CAG-83 sp900547745	79.6404	209	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_018228685.1	s__CAG-83 sp001916855	79.6379	219	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCA_000435975.1	s__CAG-83 sp000435975	79.6097	190	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
GCA_900550585.1	s__CAG-83 sp900550585	79.532	220	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900545585.1	s__CAG-83 sp900545585	79.4485	219	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_900317425.1	s__CAG-83 sp900317425	79.2616	176	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.98	99.98	0.95	0.95	2	-
GCA_900554275.1	s__CAG-83 sp900554275	79.1549	183	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_900552725.1	s__CAG-83 sp900552725	79.0812	179	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.50	98.05	0.78	0.74	4	-
GCA_900551995.1	s__CAG-83 sp900551995	79.068	188	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	97.61	0.85	0.83	3	-
GCF_018408575.1	s__CAG-83 sp000431575	78.9343	206	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
GCA_900555735.1	s__CAG-83 sp900555735	78.9314	180	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.84	99.67	0.89	0.81	3	-
GCA_017427645.1	s__CAG-83 sp017427645	78.821	156	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552015.1	s__ER4 sp900552015	78.8137	162	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015067525.1	s__CAG-83 sp015067525	78.7402	178	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552375.1	s__ER4 sp900552375	78.5835	156	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900313295.1	s__CAG-83 sp900313295	78.4001	155	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	96.38	0.88	0.79	5	-
GCA_902782615.1	s__CAG-83 sp902782615	78.229	119	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458885.1	s__ER4 sp017458885	77.7914	87	543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 16:02:29,595] [INFO] GTDB search result was written to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/result_gtdb.tsv
[2023-06-17 16:02:29,596] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:02:29,601] [INFO] DFAST_QC result json was written to GCA_905209115.1_ERR1600627-mag-bin.6_genomic.fna/dqc_result.json
[2023-06-17 16:02:29,601] [INFO] DFAST_QC completed!
[2023-06-17 16:02:29,601] [INFO] Total running time: 0h0m43s