[2024-01-25 18:15:35,562] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference
[2024-01-25 18:15:36,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,692] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb13098-5150-4dcf-8582-524b9f2b0f29/GCF_025506335.1_ASM2550633v1_genomic.fna.gz | prodigal -d GCF_025506335.1_ASM2550633v1_genomic.fna/cds.fna -a GCF_025506335.1_ASM2550633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:46,670] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:46,670] [INFO] Task started: HMMsearch
[2024-01-25 18:15:46,670] [INFO] Running command: hmmsearch --tblout GCF_025506335.1_ASM2550633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/reference_markers.hmm GCF_025506335.1_ASM2550633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:46,899] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:46,900] [INFO] Found 6/6 markers.
[2024-01-25 18:15:46,934] [INFO] Query marker FASTA was written to GCF_025506335.1_ASM2550633v1_genomic.fna/markers.fasta
[2024-01-25 18:15:46,934] [INFO] Task started: Blastn
[2024-01-25 18:15:46,934] [INFO] Running command: blastn -query GCF_025506335.1_ASM2550633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/reference_markers.fasta -out GCF_025506335.1_ASM2550633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:48,044] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:48,047] [INFO] Selected 25 target genomes.
[2024-01-25 18:15:48,047] [INFO] Target genome list was writen to GCF_025506335.1_ASM2550633v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:48,068] [INFO] Task started: fastANI
[2024-01-25 18:15:48,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb13098-5150-4dcf-8582-524b9f2b0f29/GCF_025506335.1_ASM2550633v1_genomic.fna.gz --refList GCF_025506335.1_ASM2550633v1_genomic.fna/target_genomes.txt --output GCF_025506335.1_ASM2550633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:08,745] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:08,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:08,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:08,760] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:16:08,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:16:08,760] [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
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	81.2174	773	1362	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	79.1114	508	1362	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	79.0206	470	1362	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	78.9227	488	1362	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	78.8551	468	1362	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	78.8426	467	1362	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	78.8369	482	1362	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	78.7704	490	1362	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	78.7554	467	1362	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	78.7285	441	1362	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.3499	448	1362	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	78.3028	501	1362	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	78.1836	485	1362	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	78.134	492	1362	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	78.1241	433	1362	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	78.1023	489	1362	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	78.0989	435	1362	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.0895	450	1362	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	78.0574	441	1362	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.0055	462	1362	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	77.9438	433	1362	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.883	462	1362	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	77.0433	262	1362	95	below_threshold
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	76.7211	351	1362	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	76.4476	357	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:08,763] [INFO] DFAST Taxonomy check result was written to GCF_025506335.1_ASM2550633v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:08,763] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:08,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:08,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/checkm_data
[2024-01-25 18:16:08,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:08,805] [INFO] Task started: CheckM
[2024-01-25 18:16:08,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025506335.1_ASM2550633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025506335.1_ASM2550633v1_genomic.fna/checkm_input GCF_025506335.1_ASM2550633v1_genomic.fna/checkm_result
[2024-01-25 18:16:58,952] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:58,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:58,971] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:58,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:58,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025506335.1_ASM2550633v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:58,972] [INFO] Task started: Blastn
[2024-01-25 18:16:58,972] [INFO] Running command: blastn -query GCF_025506335.1_ASM2550633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg123d1a24-5bcb-47ea-8ae8-d50ce7480156/dqc_reference/reference_markers_gtdb.fasta -out GCF_025506335.1_ASM2550633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:00,816] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:00,819] [INFO] Selected 18 target genomes.
[2024-01-25 18:17:00,819] [INFO] Target genome list was writen to GCF_025506335.1_ASM2550633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:00,834] [INFO] Task started: fastANI
[2024-01-25 18:17:00,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb13098-5150-4dcf-8582-524b9f2b0f29/GCF_025506335.1_ASM2550633v1_genomic.fna.gz --refList GCF_025506335.1_ASM2550633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025506335.1_ASM2550633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:14,926] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:14,937] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:17:14,937] [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_014127285.1	s__Mumia sp014127285	86.2467	1148	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	99.73	99.46	0.99	0.98	3	-
GCF_010994095.1	s__Mumia xiangluensis	83.3608	1012	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002797495.1	s__Mumia flava	81.2001	775	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336805.1	s__Aeromicrobium sp004336805	79.3655	481	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312105.1	s__Aeromicrobium massiliense	79.1291	505	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428805.1	s__Aeromicrobium sp001428805	79.1155	478	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992115.1	s__Aeromicrobium flavum	79.0774	420	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	78.9153	502	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_001509405.1	s__Aeromicrobium erythreum	78.8306	471	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.57	98.39	0.93	0.92	6	-
GCF_013408555.1	s__Aeromicrobium tamlense	78.8202	469	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	78.3723	516	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	78.3582	484	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127485.1	s__Nocardioides sp014127485	78.2986	501	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_001428125.1	s__Nocardioides sp001428125	78.1845	436	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695785.1	s__JACCZT01 sp013695785	78.1085	274	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	78.0147	470	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018672315.1	s__Nocardioides_A sp018672315	77.8691	397	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	76.8462	329	1362	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:14,939] [INFO] GTDB search result was written to GCF_025506335.1_ASM2550633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:14,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:14,943] [INFO] DFAST_QC result json was written to GCF_025506335.1_ASM2550633v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:14,943] [INFO] DFAST_QC completed!
[2024-01-25 18:17:14,943] [INFO] Total running time: 0h1m39s