[2024-01-24 13:57:26,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:26,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:26,394] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference
[2024-01-24 13:57:27,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:27,684] [INFO] Task started: Prodigal
[2024-01-24 13:57:27,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b20515e-43ee-4dee-af14-532a04ef8dd7/GCF_000156535.1_ASM15653v1_genomic.fna.gz | prodigal -d GCF_000156535.1_ASM15653v1_genomic.fna/cds.fna -a GCF_000156535.1_ASM15653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:38,315] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:38,316] [INFO] Task started: HMMsearch
[2024-01-24 13:57:38,316] [INFO] Running command: hmmsearch --tblout GCF_000156535.1_ASM15653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/reference_markers.hmm GCF_000156535.1_ASM15653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:38,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:38,623] [INFO] Found 6/6 markers.
[2024-01-24 13:57:38,663] [INFO] Query marker FASTA was written to GCF_000156535.1_ASM15653v1_genomic.fna/markers.fasta
[2024-01-24 13:57:38,663] [INFO] Task started: Blastn
[2024-01-24 13:57:38,664] [INFO] Running command: blastn -query GCF_000156535.1_ASM15653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/reference_markers.fasta -out GCF_000156535.1_ASM15653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:39,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:39,328] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:39,329] [INFO] Target genome list was writen to GCF_000156535.1_ASM15653v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:39,333] [INFO] Task started: fastANI
[2024-01-24 13:57:39,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b20515e-43ee-4dee-af14-532a04ef8dd7/GCF_000156535.1_ASM15653v1_genomic.fna.gz --refList GCF_000156535.1_ASM15653v1_genomic.fna/target_genomes.txt --output GCF_000156535.1_ASM15653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:54,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:54,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:54,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:54,245] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:57:54,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:54,245] [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
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	100.0	1420	1424	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	99.8774	1410	1424	95	conclusive
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	99.8745	1411	1424	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	82.7827	409	1424	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	81.4438	261	1424	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	81.1336	405	1424	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.5881	135	1424	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	79.1065	126	1424	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	78.9579	96	1424	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.8693	164	1424	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.3639	212	1424	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.3557	109	1424	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.332	68	1424	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.922	63	1424	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.8406	67	1424	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.7413	83	1424	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.4428	65	1424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,246] [INFO] DFAST Taxonomy check result was written to GCF_000156535.1_ASM15653v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:54,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:54,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:54,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/checkm_data
[2024-01-24 13:57:54,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:54,292] [INFO] Task started: CheckM
[2024-01-24 13:57:54,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000156535.1_ASM15653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000156535.1_ASM15653v1_genomic.fna/checkm_input GCF_000156535.1_ASM15653v1_genomic.fna/checkm_result
[2024-01-24 13:58:31,982] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:31,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,003] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:32,003] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:32,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000156535.1_ASM15653v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:32,004] [INFO] Task started: Blastn
[2024-01-24 13:58:32,004] [INFO] Running command: blastn -query GCF_000156535.1_ASM15653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7d18904-31e5-4a5b-93dc-8b19e169623b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000156535.1_ASM15653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:33,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:33,131] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:33,132] [INFO] Target genome list was writen to GCF_000156535.1_ASM15653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:33,145] [INFO] Task started: fastANI
[2024-01-24 13:58:33,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b20515e-43ee-4dee-af14-532a04ef8dd7/GCF_000156535.1_ASM15653v1_genomic.fna.gz --refList GCF_000156535.1_ASM15653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000156535.1_ASM15653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:44,630] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:44,647] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:44,647] [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_900537995.1	s__Roseburia intestinalis	99.8774	1410	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	conclusive
GCA_003483745.1	s__Roseburia sp003483745	91.1655	808	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCF_003470905.1	s__Roseburia sp003470905	90.8075	1020	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCF_000174195.1	s__Roseburia inulinivorans	82.8266	409	1424	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_000225345.1	s__Roseburia hominis	81.1078	406	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_900550935.1	s__Roseburia sp900550935	79.6588	365	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_900542495.1	s__Roseburia sp900542495	78.9706	329	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCA_900753715.1	s__Roseburia sp900753715	78.6163	291	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.04	99.04	0.83	0.83	2	-
GCA_900771955.1	s__CAG-45 sp900771955	78.4217	187	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695765.1	s__VUNI01 sp009695765	78.4174	211	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315735.1	s__RUG115 sp900315735	78.0006	182	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
GCA_017626625.1	s__Roseburia sp017626625	77.9734	180	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937095.1	s__Roseburia sp017937095	77.9545	246	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782995.1	s__RUG115 sp902782995	77.7261	170	1424	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:44,649] [INFO] GTDB search result was written to GCF_000156535.1_ASM15653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:44,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:44,653] [INFO] DFAST_QC result json was written to GCF_000156535.1_ASM15653v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:44,653] [INFO] DFAST_QC completed!
[2024-01-24 13:58:44,653] [INFO] Total running time: 0h1m18s